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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/seqprep">Debian Med / seqprep</a>
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Commits:
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<strong><a href="https://salsa.debian.org/med-team/seqprep/-/commit/8db0a1de9c9abde0d4fd4541e162768d7cac56ad">8db0a1de</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-03-12T18:43:10+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not generate README.html during build
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<strong><a href="https://salsa.debian.org/med-team/seqprep/-/commit/314202b3e8c26e937d944172382f46c4dc18a419">314202b3</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-03-12T18:43:47+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Addnotate python3 with nocheck since it is a test-only B-D
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<strong><a href="https://salsa.debian.org/med-team/seqprep/-/commit/050091a8dd33849f07f7040e7b57648fcbb3d527">050091a8</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-03-12T18:44:16+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add myself to uploaders
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<h4>3 changed files:</h4>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap. When an adapter sequence is present, that means that the two reads must overlap (in most cases) so they are forcefully merged. When reads do not have adapter sequence they must be treated with care when doing the merging, so a much more specific approach is taken. The default parameters were chosen with specificity in mind, so that they could be ran on libraries where very few reads are expected to overlap. It is always safest though to save the overlapping procedure for libraries where you have some prior knowledge that a significant portion of the reads will have some overlap. <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Before running SeqPrep make sure to check that the program's defaults are indeed the adapters you are looking for. Try copying the default forward adapter from this file and grep it against your reads doing a word count, also try the same with the reverse adapter with grep. You should see some hits. You can also try using (and validating with grep) <span class="nt" style="color: #000080;"><code></span>-A GATCGGAAGAGCACACG -B AGATCGGAAGAGCGTCGT<span class="nt" style="color: #000080;"></code></span> as parameters. To find a list of Illumina adapter sequences you should write to Illumina tech support TechSupport@illumina.com (they do not like people to share the list of sequences outside of their institution).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Chose about 20bp of an adapter sequence where:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="html"><span class="nt" style="color: #000080;"><ol></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>You see the most hits with grep<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>When you run a command like <span class="nt" style="color: #000080;"><code></span>zcat Lane2_0d_2.fastq.gz | head -n 1000000 |grep "INSERT ADAPTER HERE" | head<span class="nt" style="color: #000080;"></code></span> you see the adapter sequence show up at the beginning of a few reads. Also the -A and -B arguments should be as they show up in your data, SeqPrep searches directly for these sequences without doing reverse complementing.<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>Check the forward and reverse and make sure that you have roughly the same number of hits via a command to count hits like: <span class="nt" style="color: #000080;"><code></span>zcat Lane2_0d_2.fastq.gz | head -n 1000000 |grep "INSERT ADAPTER HERE" | wc -l<span class="nt" style="color: #000080;"></code></li></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>As an additional precaution, the program checks for good read overlap once the adapters are trimmed. If the adapter is trimmed and the reads do not have a reasonable adapter overlap (you can modify this setting with -X) then the reads aren't printed or merged. <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>See <span class="nt" style="color: #000080;"><code></span>Test/README.md<span class="nt" style="color: #000080;"></code></span> for some information on testing out other parameters. <span class="nt" style="color: #000080;"><code></span>Test/SimTest<span class="nt" style="color: #000080;"></code></span> has some particularly cool test data which you can use to check out sensitivity and specificity of adapter trimming using different parameters. The results of the test are displayed in <span class="nt" style="color: #000080;"><code></span>results.html<span class="nt" style="color: #000080;"></code></span> which uses the google charts API so that the points are interactive and you can easily determine which settings made which points.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Usage:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>./SeqPrep [Required Args] [Options]</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="html">NOTE 1: The output is always gziped compressed.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="html">NOTE 2: If the quality strings in the output contain characters less than ascii 33 on an ascii table (they look like lines from a binary file), try running again with or without the -6 option.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Required Arguments:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-f <span class="ni" style="color: #800080;"><</span>first read input fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="html">-r <span class="ni" style="color: #800080;"><</span>second read input fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="html">-1 <span class="ni" style="color: #800080;"><</span>first read output fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="html">-2 <span class="ni" style="color: #800080;"><</span>second read output fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>General Arguments (Optional):<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-3 <span class="ni" style="color: #800080;"><</span>first read discarded fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="html">-4 <span class="ni" style="color: #800080;"><</span>second read discarded fastq filename<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="html">-h Display this help message and exit (also works with no args) </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="html">-6 Input sequence is in phred+64 rather than phred+33 format, the output will still be phred+33 </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="html">-q <span class="ni" style="color: #800080;"><</span>Quality score cutoff for mismatches to be counted in overlap; default = 13<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="html">-L <span class="ni" style="color: #800080;"><</span>Minimum length of a trimmed or merged read to print it; default = 30<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Arguments for Adapter/Primer Trimming (Optional):<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-A <span class="ni" style="color: #800080;"><</span>forward read primer/adapter sequence to trim as it would appear at the end of a read (recommend about 20bp of this)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="html"> (should validate by grepping a file); default (genomic non-multiplexed adapter1) = AGATCGGAAGAGCGGTTCAG<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="html">-B <span class="ni" style="color: #800080;"><</span>reverse read primer/adapter sequence to trim as it would appear at the end of a read (recommend about 20bp of this)</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="html"> (should validate by grepping a file); default (genomic non-multiplexed adapter2) = AGATCGGAAGAGCGTCGTGT<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="html">-O <span class="ni" style="color: #800080;"><</span>minimum overall base pair overlap with adapter sequence to trim; default = 10<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="html">-M <span class="ni" style="color: #800080;"><</span>maximum fraction of good quality mismatching bases for primer/adapter overlap; default = 0.020000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="html">-N <span class="ni" style="color: #800080;"><</span>minimum fraction of matching bases for primer/adapter overlap; default = 0.870000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="html">-b <span class="ni" style="color: #800080;"><</span>adapter alignment band-width; default = 50<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="html">-Q <span class="ni" style="color: #800080;"><</span>adapter alignment gap-open; default = 8<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="html">-t <span class="ni" style="color: #800080;"><</span>adapter alignment gap-extension; default = 2<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="html">-e <span class="ni" style="color: #800080;"><</span>adapter alignment gap-end; default = 2<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="html">-Z <span class="ni" style="color: #800080;"><</span>adapter alignment minimum local alignment score cutoff [roughly (2*num_hits) - (num_gaps*gap_open) - (num_gaps*gap_close) - (gap_len*gap_extend) - (2*num_mismatches)]; default = 26<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="html">-w <span class="ni" style="color: #800080;"><</span>read alignment band-width; default = 50<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="html">-W <span class="ni" style="color: #800080;"><</span>read alignment gap-open; default = 26<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="html">-p <span class="ni" style="color: #800080;"><</span>read alignment gap-extension; default = 9<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="html">-P <span class="ni" style="color: #800080;"><</span>read alignment gap-end; default = 5<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="html">-X <span class="ni" style="color: #800080;"><</span>read alignment maximum fraction gap cutoff; default = 0.125000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="html">-z <span class="ni" style="color: #800080;"><</span>use mask; N will replace adapters<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Optional Arguments for Merging:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-y <span class="ni" style="color: #800080;"><</span>maximum quality score in output ((phred 33) default = ']' )<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="html">-g <span class="ni" style="color: #800080;"><</span>print overhang when adapters are present and stripped (use this if reads are different length)<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="html">-s <span class="ni" style="color: #800080;"><</span>perform merging and output the merged reads to this file<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="html">-E <span class="ni" style="color: #800080;"><</span>write pretty alignments to this file for visual Examination<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="html">-x <span class="ni" style="color: #800080;"><</span>max number of pretty alignments to write (if -E provided); default = 10000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="html">-o <span class="ni" style="color: #800080;"><</span>minimum overall base pair overlap to merge two reads; default = 15<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="html">-m <span class="ni" style="color: #800080;"><</span>maximum fraction of good quality mismatching bases to overlap reads; default = 0.020000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="html">-n <span class="ni" style="color: #800080;"><</span>minimum fraction of matching bases to overlap reads; default = 0.900000<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>My current strategy to deal with ambiguous alignments to low complexity regions is as follows:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="html"><span class="nt" style="color: #000080;"><ol></span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>I have some minimum requirements for an overlap to be accepted<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>After the first one is found (ie the one with the maximal overlap between the two sequences), if low complexity filtering is enabled, I keep searching<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="html"><span class="nt" style="color: #000080;"><li></span>if a second viable hit is found, I give up and say that it is not a good idea to merge the two reads.<span class="nt" style="color: #000080;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="html"><span class="nt" style="color: #000080;"></ol></span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>I check for ambiguous alignments in read overlapping, but not in adapter trimming where the most conservative thing to do is strip the most aggressively aligned adapter (The closest to the beginning of the read).<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>To accept an alignment I allow some fraction of mismatches (currently the floor of 0.06 of the alignment length for adapter and 0.02 of the alignment length for two reads). That means that in most cases for overlapping two reads I don't allow any mismatches between adjacent reads, but if there is a 50bp potential overlap with 1 mismatch over q20 for example, I allow it. Anything below 50 needs to be perfect other than with low quality bases.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Since we ignore poor quality bases, we could have the case where a single real match followed by a long string of poor quality bases to the end of the read would result in a called overlap. That seemed like a bad idea. To get around that I require that at least some fraction of the overlapping length be matches. Right now I have that parameter set at 0.7 for adapter trimming and 0.75 for read merging, so for a case where only the last 10 bases overlap, at least 7 of those must be matches. <span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Since doing that many floating point multiplications seems like a bad idea, I just have a table that pre-calculates all of those min matches and max mismatch numbers for every overlap length up to the maximum allowed read length.<span class="nt" style="color: #000080;"></p></span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="html"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Finally I have a parameter you can set which specifies a minimum resulting read length after adapter trimming and/or merging so that ultra short trimmed reads aren't output.<span class="nt" style="color: #000080;"></p></span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="html"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Following are results from hand testing the three main merge cases. Now to generate similar output automatically just supply the <span class="nt" style="color: #000080;"><code></span>-E readable_alignment.txt.gz<span class="nt" style="color: #000080;"></code></span> argument to the program (the output is gzip compressed into the file name specified). <span class="nt" style="color: #000080;"></p></span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="html"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Sequence Merge No Adapter Present:<span class="nt" style="color: #000080;"></p></span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="html"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>QUER: NCCTGCTACTACCACCCGTTCCGTGCCTGGAGCCTGCATGTTGGGCAGATACGTGCTGCCACAGCCTGTCTCTGCTGGTGCCTGGGCCTC</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="html"> || |||||||||||| || | |||||||||||||||||||||||||||||||||</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="html">SUBJ: TGTGTGTTGGGCAGATGCGGGGGGCCACAGCCTGTCTCTGCTGGTGCCTGGGCCTCTCCTGTTCCTTGCCCACGTCTCCGTCTCCTGTTG</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="html">RESU: NCCTGCTACTACCACCCGTTCCGTGCCTGGAGCCTGCATGTTGGGCAGATACGTGCTGCCACAGCCTGTCTCTGCTGGTGCCTGGGCCTCTCCTGTTCCTTGCCCACGTCTCCGTCTCCTGTTG</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="html">Quality Merge:</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="html">QUER: !223387787@@@CCC22C@@@@@@@@@@@@@@@@@@@@@@@@@@@@?@@89887:::::.2125@@:@@:::::@@@@@<span class="ni" style="color: #800080;"><<</span>::8@@@@@</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="html">SUBJ: !!!!!!!!!!!!!!!!!!!!!!!!!!!@@@8DEGE@EDDBB2<span class="ni" style="color: #800080;"><</span>BBE@EHBFE@EE<span class="ni" style="color: #800080;">></span>D8@DBE<span class="ni" style="color: #800080;">></span>BFIDH@IIEEIIBEIEIIGBIIGIFII</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="html">RESU: !223387787@@@CCC22C@@@@@@@@@@@@@@@@@@@@@@@@@@@@?@@89887:::::.QPQLSSSSSSSSSSQSSSSSSSSSSSSSSD8@DBE<span class="ni" style="color: #800080;">></span>BFIDH@IIEEIIBEIEIIGBIIGIFII</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="html"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Sequence Merge Adapter Present, Easy Peezy Mode (same lengths):<span class="nt" style="color: #000080;"></p></span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>SUBJ: NGATATGATTCCCAATCTAAGCAAACTGTCATGGAAAC</span>
</pre>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="html"> |||||||||||||||||||||||||||||||||||||</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="html">QUER: GGATATGATTCCCAATCTAAGCAAACTGTCATGGAAAC</span>
</pre>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="html">RESU: GGATATGATTCCCAATCTAAGCAAACTGTCATGGAAAC</span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="html">Quality Merge:</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="html">SUBJ: !.-/.53444@@@@@@@@@@@@@@@@@@@@@@@@@@@@</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="html">QUER: IHGIIIDIIHGEHIGHIFHIFIIIIHIIIIIIIIIHII</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="html">RESU: ISSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Sequence merge Adapter but lengths differ:<span class="nt" style="color: #000080;"></p></span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>SUBJ: AATTGATGGGTGCCCACCCACGGGCCAGACAAAATCATCTGGCAAGCTGGATGCAGCCTACAAGCTGTAAGATTGGA</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="html"> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="html">QUER: AATTGATGGGTGCCCACCCACGGGCCAGACAAAATCATCTGGCAAGCTGGATGCAGCCTACAAGCTGTA</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="html">RESU: AATTGATGGGTGCCCACCCACGGGCCAGACAAAATCATCTGGCAAGCTGGATGCAGCCTACAAGCTGTAAGATTGGA</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="html">Quality Merge:</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="html">SUBJ: =DEC??DDBD?4B=BEE@@@GB<span class="ni" style="color: #800080;">></span>GEE:DE8=2::6GDGBGEGDD<span class="ni" style="color: #800080;"><</span>=;A?=AGGGG=5.=<span class="ni" style="color: #800080;"><</span>BD?B?DDB<span class="ni" style="color: #800080;">></span>B4725:E<span class="ni" style="color: #800080;">></span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="html">QUER: GDDBBFBGGFBHFIEDGGGBDGGG<span class="ni" style="color: #800080;"><</span>GGDDG@IIIEIHDIHGIIIDDGDGDFDIFIHGIDEGGGDIIIGI</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="html">RESU: SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSB4725:E<span class="ni" style="color: #800080;">></span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="html"><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>If interested there is a website where I post my tests of different parameters for SeqPrep on simulated data. There are also a few comparison stats of different programs to trim adapters. The website can be accessed here:</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="html">http://hgwdev.cse.ucsc.edu/~jstjohn/seqprep/<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>where the pages are named <span class="nt" style="color: #000080;"><code></span>result(date).html<span class="nt" style="color: #000080;"></code></span>. The latest ones (as of when I have gotten around to edit this) can be found here:<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>http://hgwdev.cse.ucsc.edu/~jstjohn/seqprep/results2011-09-15.html<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Note that although my program is more sensitive and specific than fastq-clipper, I optimized my default parameters based on this test. Results on real data may be</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="html">different, although I believe my method takes advantage of a more realistic adapter model than other software does. For example, even though my program requires</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="html">10bp of adapter to be present at the end of a read to trim it off (by default) there is a backup adapter trimming function that trimms based on strong and</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="html">unambiguous read overlap. Because of this my program can trim the adapter even if it is only present in the last few bases of the read.<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Also note that fastq-mcf appears to do a little better at sensitivity (0.992 vs 0.985) at a very large cost to specificity (0.497 vs 0.994).<span class="nt" style="color: #000080;"></p></span></span></pre>
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<a href="https://salsa.debian.org/med-team/seqprep/-/compare/47fd208e83c759f85d488e7fd0d2dcbb9c33ac43...050091a8dd33849f07f7040e7b57648fcbb3d527#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: seqprep</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Tim Booth <tbooth@ceh.ac.uk>,</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org>,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Nilesh Patra <nilesh@debian.org></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 12),</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> markdown,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> python3 <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/seqprep</span>
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<a href="https://salsa.debian.org/med-team/seqprep/-/compare/47fd208e83c759f85d488e7fd0d2dcbb9c33ac43...050091a8dd33849f07f7040e7b57648fcbb3d527#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> cp SeqPrep seqprep</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> m<span class="idiff left right">arkdown README.md > </span>README.html</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> m<span class="idiff left">v ${CURDIR}/debian/</span>README.html<span class="idiff right"> ${CURDIR}</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_clean:</span>
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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh_clean</span>
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