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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/qiime">Debian Med / qiime</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/qiime/commit/1ae71cf2f21289d4ef3519b994888c256166017a">1ae71cf2</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2019-03-11T22:16:02Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Delete old Qiime dependencies
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/qiime/commit/1ae71cf2f21289d4ef3519b994888c256166017a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">qiime (2019.1.0-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Delete old Qiime dependencies</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Tue, 12 Mar 2019 00:13:16 +0200</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">qiime (2019.1.0-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<a href="https://salsa.debian.org/med-team/qiime/commit/1ae71cf2f21289d4ef3519b994888c256166017a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -27,77 +27,30 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">bibtexparser</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">decorator</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> python3-matplotlib,</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> python3-numpy,</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pandas</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">tzlocal</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">yaml</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> python-burrito,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> python-burrito-fillings (>= 0.1.1),</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> python-biom-format,</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> python-cogent (>= 1.5.3),</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> python-mpi4py,</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> python-qcli,</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> pynast (>= 1.2.2),</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> qiime-data,</span>
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<td class="diff-line-num old old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> ampliconnoise,</span>
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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> blast2 | blast+-legacy,</span>
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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> bwa,</span>
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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> cd-hit,</span>
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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> chimeraslayer,</span>
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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> clearcut,</span>
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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> clustalw,</span>
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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> ea-utils,</span>
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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> emperor (>= 0.9.51),</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> fasttree,</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> infernal,</span>
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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> libjs-jquery,</span>
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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> mafft,</span>
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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> muscle,</span>
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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> parsinsert,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> raxml,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
59
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> r-cran-optparse,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
60
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> rdp-classifier,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
61
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> seqprep,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
62
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> sortmerna,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
63
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<td class="diff-line-num new_line old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> sumatra,</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> swarm,</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> vsearch</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">Recommends: mothur,</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> rtax</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">Suggests: t-coffee,</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> cytoscape,</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> torque-client,</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> qiime-default-reference</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pyparsing</span><span class="p">,</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">dateutil</span></span>
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72
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">Quantitative</span> <span class="n" style="color: #333;">Insights</span> <span class="n" style="color: #333;">Into</span> <span class="n" style="color: #333;">Microbial</span> <span class="n" style="color: #333;">Ecology</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> QIIME (canonically pronounced ‘Chime’) is a pipeline for performing</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> microbial community analysis that integrates many third party tools which</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> have become standard in the field. A standard QIIME analysis begins with</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> sequence data from one or more sequencing platforms, including</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> * Sanger,</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> * Roche/454, and</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> * Illumina GAIIx.</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> QIIME can perform:</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> * library de-multiplexing and quality filtering;</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> * denoising with PyroNoise;</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> * OTU and representative set picking with uclust, cdhit, mothur, BLAST,</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> or other tools;</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"> * taxonomy assignment with BLAST or the RDP classifier;</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> * sequence alignment with PyNAST, muscle, infernal, or other tools;</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"> * phylogeny reconstruction with FastTree, raxml, clearcut, or other tools;</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"> * alpha diversity and rarefaction, including visualization of results,</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"> using over 20 metrics including Phylogenetic Diversity, chao1, and</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext"> observed species;</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"> * beta diversity and rarefaction, including visualization of results,</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"> using over 25 metrics including weighted and unweighted UniFrac,</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"> Euclidean distance, and Bray-Curtis;</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"> * summarization and visualization of taxonomic composition of samples</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"> using pie charts and histograms</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"> and many other features.</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">researchers</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">start</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">analysis</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">raw</span> <span class="n" style="color: #333;">DNA</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">finish</span> <span class="k" style="font-weight: 600;">with</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"> <span class="n" style="color: #333;">publication</span><span class="p">-</span><span class="n" style="color: #333;">quality</span> <span class="n" style="color: #333;">figures</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">statistical</span> <span class="n" style="color: #333;">results</span><span class="p">.</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"> <span class="n" style="color: #333;">Key</span> <span class="n" style="color: #333;">features</span><span class="p">:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Integrated</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">automatic</span> <span class="n" style="color: #333;">tracking</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">data</span> <span class="n" style="color: #333;">provenance</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Semantic</span> <span class="n" style="color: #333;">type</span> <span class="nf" style="color: #900; font-weight: 600;">system</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Plugin</span> <span class="nf" style="color: #900; font-weight: 600;">system</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">extending</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">functionality</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">types</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">user</span> <span class="n" style="color: #333;">interfaces</span> <span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">g</span><span class="p">.</span> <span class="n" style="color: #333;">API</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">command</span> <span class="n" style="color: #333;">line</span><span class="p">,</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">graphical</span><span class="p">)</span></span>
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97
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="mosel"> <span class="p">.</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"> QIIME includes parallelization capabilities for many of the</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> computationally intensive steps. By default, these are configured to</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"> utilize a mutli-core environment, and are easily configured to run in</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"> a cluster environment. QIIME is built in Python using the open-source</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"> PyCogent toolkit. It makes extensive use of unit tests, and is highly</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"> modular to facilitate custom analyses.</span></pre>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">redesign</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">rewrite</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">address</span> <span class="n" style="color: #333;">many</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limitations</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">while</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">retaining</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">features</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">makes</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">1</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">widely</span><span class="p">-</span><span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">analysis</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"> <span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">supports</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">initial</span> <span class="k" style="font-weight: 600;">end</span><span class="p">-</span><span class="k" style="font-weight: 600;">to</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">New</span> <span class="n" style="color: #333;">functionality</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">regularly</span> <span class="n" style="color: #333;">become</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">through</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugins</span><span class="p">.</span> <span class="n" style="color: #333;">You</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">view</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">currently</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="n" style="color: #333;">availability</span> <span class="n" style="color: #333;">page</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">page</span> <span class="n" style="color: #333;">lists</span> <span class="n" style="color: #333;">plugins</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">being</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"> <span class="n" style="color: #333;">developed</span><span class="p">.</span> </span></pre>
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