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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bbmap">Debian Med / bbmap</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bbmap/commit/74c7513c30f9deeafc6d8ebde58153aa08371e45">74c7513c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-04-05T22:19:13Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage for dedupe.sh
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<h4>1 changed file:</h4>
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+
debian/mans/dedupe.sh.1
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<h4>Changes:</h4>
<li id="d864ddf62aef569bfeed5f2b1577c945be7a286c">
<a href="https://salsa.debian.org/med-team/bbmap/commit/74c7513c30f9deeafc6d8ebde58153aa08371e45#d864ddf62aef569bfeed5f2b1577c945be7a286c"><strong>debian/mans/dedupe.sh.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH DEDUPE.SH "1" "April 2019" "dedupe.sh 38.43" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">dedupe.sh \- Simplifies assemblies by removing duplicate or contained</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B dedupe.sh</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,in=<file or stdin> out=<file or stdout>\/\fR</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Accepts one or more files containing sets of sequences (reads or scaffolds).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Removes duplicate sequences, which may be specified to be exact matches, subsequences, or sequences within some percent identity.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Can also find overlapping sequences and group them into clusters.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Please read bbmap/docs/guides/DedupeGuide.txt for more information.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SH EXAMPLES</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">An example of running Dedupe for clustering short reads:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">dedupe.sh in=x.fq am=f ac=f fo c pc rnc=f mcs=4 mo=100 s=1 pto cc qin=33 csf=stats.txt pattern=cluster_%.fq dot=graph.dot</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Input may be fasta or fastq, compressed or uncompressed.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Output may be stdout or a file. With no output parameter, data will be written to stdout.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">If 'out=null', there will be no output, but statistics will still be printed.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">You can also use 'dedupe <infile> <outfile>' without the 'in=' and 'out='.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.SS I/O parameters</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">in=<file,file></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">A single file or a comma\-delimited list of files.</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">out=<file></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Destination for all output contigs.</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">pattern=<file></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Clusters will be written to individual files, where the '%' symbol in the pattern is replaced by cluster number.</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">outd=<file></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Optional; removed duplicates will go here.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.TP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">csf=<file></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">(clusterstatsfile) Write a list of cluster names and sizes.</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">dot=<file></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">(graph) Write a graph in dot format. Requires 'fo' and 'pc' flags.</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">threads=auto</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">(t) Set number of threads to use; default is number of logical processors.</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">overwrite=t</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">(ow) Set to false to force the program to abort rather than overwrite an existing file.</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.TP</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">showspeed=t</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">(ss) Set to 'f' to suppress display of processing speed.</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">minscaf=0</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">(ms) Ignore contigs/scaffolds shorter than this.</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">interleaved=auto</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">If true, forces fastq input to be paired and interleaved.</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.TP</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">ziplevel=2</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.SS Output format parameters</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">storename=t</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">(sn) Store scaffold names (set false to save memory).</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">.TP</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">#addpairnum=f</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Add .1 and .2 to numeric id of read1 and read2.</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">storequality=t</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">(sq) Store quality values for fastq assemblies (set false to save memory).</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.TP</span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">uniquenames=t</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">(un) Ensure all output scaffolds have unique names. Uses more memory.</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">numbergraphnodes=t</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">(ngn) Label dot graph nodes with read numbers rather than read names.</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">sort=f</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Sort output (otherwise it will be random). Options:</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.IP</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">length: Sort by length</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.IP</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">quality: Sort by quality</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.IP</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">name: Sort by name</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.IP</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">id: Sort by input order</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">ascending=f</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">Sort in ascending order.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.TP</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">ordered=f</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Output sequences in input order. Equivalent to sort=id ascending.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
</pre>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">renameclusters=f</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">(rnc) Rename contigs to indicate which cluster they are in.</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">.TP</span>
</pre>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">printlengthinedges=f</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">(ple) Print the length of contigs in edges.</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.SS Processing parameters</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.TP</span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">absorbrc=t</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">(arc) Absorb reverse\-complements as well as normal orientation.</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">absorbmatch=t</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">(am) Absorb exact matches of contigs.</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">absorbcontainment=t</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">(ac) Absorb full containments of contigs.</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">.TP</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">#absorboverlap=f</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">(ao) Absorb (merge) non\-contained overlaps of contigs (TODO).</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">.TP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">findoverlap=f</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">(fo) Find overlaps between contigs (containments and non\-containments). Necessary for clustering.</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.TP</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">uniqueonly=f</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">(uo) If true, all copies of duplicate reads will be discarded, rather than keeping 1.</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.TP</span>
</pre>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">rmn=f</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">(requirematchingnames) If true, both names and sequence must match.</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.TP</span>
</pre>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">usejni=f</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">(jni) Do alignments in C code, which is faster, if an edit distance is allowed.</span>
</pre>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">This will require compiling the C code; details are in \fI\,/jni/README.txt\/\fP.</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.SS Subset parameters</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">.TP</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">subsetcount=1</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">(sstc) Number of subsets used to process the data; higher uses less memory.</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.TP</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">subset=0</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">(sst) Only process reads whose ((ID%subsetcount)==subset).</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">.SS Clustering parameters</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.TP</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">cluster=f</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">(c) Group overlapping contigs into clusters.</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">.TP</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">pto=f</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">(preventtransitiveoverlaps) Do not look for new edges between nodes in the same cluster.</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.TP</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">minclustersize=1</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">(mcs) Do not output clusters smaller than this.</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">.TP</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">pbr=f</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">(pickbestrepresentative) Only output the single highest\-quality read per cluster.</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">.SS Cluster postprocessing parameters</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">.TP</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">processclusters=f</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">(pc) Run the cluster processing phase, which performs the selected operations in this category.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">For example, pc AND cc must be enabled to perform cc.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.TP</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">fixmultijoins=t</span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">(fmj) Remove redundant overlaps between the same two contigs.</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">.TP</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">removecycles=t</span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">(rc) Remove all cycles so clusters form trees.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.TP</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">cc=t</span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">(canonicizeclusters) Flip contigs so clusters have a single orientation.</span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">.TP</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">fcc=f</span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">(fixcanoncontradictions) Truncate graph at nodes with canonization disputes.</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">.TP</span>
</pre>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">foc=f</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">(fixoffsetcontradictions) Truncate graph at nodes with offset disputes.</span>
</pre>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">.TP</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">mst=f</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">(maxspanningtree) Remove cyclic edges, leaving only the longest edges that form a tree.</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">.SS Overlap Detection Parameters</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">.TP</span>
</pre>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">exact=t</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">(ex) Only allow exact symbol matches. When false, an 'N' will match any symbol.</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">.TP</span>
</pre>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">touppercase=t</span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">(tuc) Convert input bases to upper\-case; otherwise, lower\-case will not match.</span>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">maxsubs=0</span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">(s) Allow up to this many mismatches (substitutions only, no indels). May be set higher than maxedits.</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">.TP</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">maxedits=0</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">(e) Allow up to this many edits (subs or indels). Higher is slower.</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">.TP</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">minidentity=100</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">(mid) Absorb contained sequences with percent identity of at least this (includes indels).</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">.TP</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">minlengthpercent=0</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">(mlp) Smaller contig must be at least this percent of larger contig's length to be absorbed.</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">.TP</span>
</pre>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">minoverlappercent=0</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">(mop) Overlap must be at least this percent of smaller contig's length to cluster and merge.</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">.TP</span>
</pre>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">minoverlap=200</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">(mo) Overlap must be at least this long to cluster and merge.</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">.TP</span>
</pre>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">depthratio=0</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">(dr) When non\-zero, overlaps will only be formed between reads with a depth ratio of at most this.</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">Should be above 1.</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">Depth is determined by parsing the read names; this information can be added</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">by running KmerNormalize (khist.sh, bbnorm.sh, or ecc.sh) with the flag 'rename'</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">.TP</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">k=31</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">Seed length used for finding containments and overlaps. Anything shorter than k will not be found.</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">.TP</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">numaffixmaps=1</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">(nam) Number of prefixes/suffixes to index per contig. Higher is more sensitive, if edits are allowed.</span>
</pre>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">.TP</span>
</pre>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">hashns=f</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">Set to true to search for matches using kmers containing Ns. Can lead to extreme slowdown in some cases.</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">.TP</span>
</pre>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">#ignoreaffix1=f</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">(ia1) Ignore first affix (for testing).</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">.TP</span>
</pre>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">#storesuffix=f</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">(ss) Store suffix as well as prefix. Automatically set to true when doing inexact matches.</span>
</pre>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">.SS Other Parameters</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">.TP</span>
</pre>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">qtrim=f</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">Set to qtrim=rl to trim leading and trailing Ns.</span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">.TP</span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">trimq=6</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">Quality trim level.</span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">.TP</span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">forcetrimleft=\-1</span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">(ftl) If positive, trim bases to the left of this position (exclusive, 0\-based).</span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">.TP</span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">forcetrimright=\-1</span>
</pre>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">(ftr) If positive, trim bases to the right of this position (exclusive, 0\-based).</span>
</pre>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">.SS Note on Proteins / Amino Acids</span>
</pre>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">Dedupe supports amino acid space via the 'amino' flag. This also changes the default kmer length to 10.</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">In amino acid mode, all flags related to canonicity and reverse\-complementation are disabled,</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">and nam (numaffixmaps) is currently limited to 2 per tip.</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">.SS Java Parameters</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">.TP</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">\fB\-Xmx\fR</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">This will set Java's memory usage, overriding autodetection.</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">\fB\-Xmx20g\fR will specify 20 gigs of RAM, and \fB\-Xmx200m\fR will specify 200 megs.</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">The max is typically 85% of physical memory.</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">.TP</span>
</pre>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">\fB\-eoom\fR</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">This flag will cause the process to exit if an out\-of\-memory exception occurs. Requires Java 8u92+.</span>
</pre>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">.TP</span>
</pre>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">\fB\-da\fR</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">Disable assertions.</span>
</pre>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">.SH AUTHOR</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">Written by Brian Bushnell and Jonathan Rood (Last modified November 20, 2017)</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">.P</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">.P</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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