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v2.8.0
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shenwei356 committed Mar 11, 2024
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Expand Up @@ -642,30 +642,23 @@ <h1 id="download">Download</h1>
<a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;user=wHF3Lm8AAAAJ&amp;citation_for_view=wHF3Lm8AAAAJ:zYLM7Y9cAGgC"><img alt="Citation Badge" src="https://api.juleskreuer.eu/citation-badge.php?doi=10.1371/journal.pone.0163962" /></a></p>
<h2 id="current-version">Current Version</h2>
<ul>
<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.7.0">SeqKit v2.7.0</a> - 2024-01-31
<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.7.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.7.0/total.svg" /></a><ul>
<li><code>seqkit</code>:<ul>
<li>Grouping subcommands in help message, which is intuitive for beginners.</li>
</ul>
</li>
<li><code>seqkit grep</code>:<ul>
<li>New flag: <code>-D/--allow-duplicated-patterns</code> for outputting records multiple times when duplicated patterns are given. <a href="https://github.com/shenwei356/seqkit/issues/427">#427</a></li>
<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.8.0">SeqKit v2.8.0</a> - 2024-03-11
<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.8.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.8.0/total.svg" /></a><ul>
<li><code>seqkit stats</code>:<ul>
<li>Add column <code>N50_num</code>, an alias of L50, <a href="https://github.com/shenwei356/seqkit/issues/15">#15</a>.</li>
</ul>
</li>
<li><code>seqkit subseq</code>:<ul>
<li>Use the ID regular expression from the option <code>--id-regexp</code> to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. <a href="https://github.com/shenwei356/seqkit/issues/432">#432</a></li>
<li><code>seqkit seq/locate/fish/watch</code>:<ul>
<li>Removing the flag <code>-V/--validate-seq-length</code>. Now the whole sequence will be checked if <code>-v/--validate-seq</code> is given.</li>
</ul>
</li>
<li><code>seqkit split/sort/shuffle</code>:<ul>
<li>When using the two-pass mode (<code>-2/--two-pass</code>), replace possible tabs in the sequence header.</li>
</ul>
</li>
<li><code>seqkit rmdup</code>:<ul>
<li>Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using <code>-D/--dup-num-file</code>. <a href="https://github.com/shenwei356/seqkit/issues/436">#436</a></li>
<li><code>seqkit amplicon</code>:<ul>
<li>Fix the speed problem, introduced in v2.7.0. <a href="https://github.com/shenwei356/seqkit/issues/439">#439</a>.</li>
<li>Slightly faster by reusing objects.</li>
</ul>
</li>
<li><code>seqkit stats</code>:<ul>
<li>New flag <code>-S/--skip-file-check</code> to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.</li>
<li><code>seqkit seq</code>:<ul>
<li>Change the threshold sequence length for parallelizing complement sequence computation, 1kb-&gt;1Mb.</li>
</ul>
</li>
</ul>
Expand All @@ -685,44 +678,44 @@ <h3 id="links">Links</h3>
<tr>
<td style="text-align: left;">Linux</td>
<td style="text-align: left;">32-bit</td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_386.tar.gz">seqkit_linux_386.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_386.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_386.tar.gz">seqkit_linux_386.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_386.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_386.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">Linux</td>
<td style="text-align: left;"><strong>64-bit</strong></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_amd64.tar.gz"><strong>seqkit_linux_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_amd64.tar.gz"><strong>seqkit_linux_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_amd64.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">Linux</td>
<td style="text-align: left;"><strong>arm64</strong></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_arm64.tar.gz"><strong>seqkit_linux_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_arm64.tar.gz"><strong>seqkit_linux_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_linux_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_linux_arm64.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">macOS</td>
<td style="text-align: left;"><strong>64-bit</strong></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_amd64.tar.gz"><strong>seqkit_darwin_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_amd64.tar.gz"><strong>seqkit_darwin_amd64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_amd64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_amd64.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">macOS</td>
<td style="text-align: left;"><strong>arm64</strong></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_arm64.tar.gz"><strong>seqkit_darwin_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_arm64.tar.gz"><strong>seqkit_darwin_arm64.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_darwin_arm64.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_darwin_arm64.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">Windows</td>
<td style="text-align: left;">32-bit</td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_386.exe.tar.gz">seqkit_windows_386.exe.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_386.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_386.exe.tar.gz">seqkit_windows_386.exe.tar.gz</a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_386.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_386.exe.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
<tr>
<td style="text-align: left;">Windows</td>
<td style="text-align: left;"><strong>64-bit</strong></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_amd64.exe.tar.gz"><strong>seqkit_windows_amd64.exe.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.7.0/seqkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_amd64.exe.tar.gz"><strong>seqkit_windows_amd64.exe.tar.gz</strong></a>, <br/> <a href="http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz">中国镜像</a></td>
<td style="text-align: left;"><a href="https://github.com/shenwei356/seqkit/releases/download/v2.8.0/seqkit_windows_amd64.exe.tar.gz"><img alt="Github Releases (by Asset)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/latest/seqkit_windows_amd64.exe.tar.gz.svg?maxAge=3600" /></a></td>
</tr>
</tbody>
</table>
Expand Down Expand Up @@ -837,6 +830,34 @@ <h2 id="shell-completion">Shell-completion</h2>
</code></pre>
<h2 id="release-history">Release history</h2>
<ul>
<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.7.0">SeqKit v2.7.0</a> - 2024-01-31
<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.7.0"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.7.0/total.svg" /></a><ul>
<li><code>seqkit</code>:<ul>
<li>Grouping subcommands in help message, which is intuitive for beginners.</li>
</ul>
</li>
<li><code>seqkit grep</code>:<ul>
<li>New flag: <code>-D/--allow-duplicated-patterns</code> for outputting records multiple times when duplicated patterns are given. <a href="https://github.com/shenwei356/seqkit/issues/427">#427</a></li>
</ul>
</li>
<li><code>seqkit subseq</code>:<ul>
<li>Use the ID regular expression from the option <code>--id-regexp</code> to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. <a href="https://github.com/shenwei356/seqkit/issues/432">#432</a></li>
</ul>
</li>
<li><code>seqkit split/sort/shuffle</code>:<ul>
<li>When using the two-pass mode (<code>-2/--two-pass</code>), replace possible tabs in the sequence header.</li>
</ul>
</li>
<li><code>seqkit rmdup</code>:<ul>
<li>Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using <code>-D/--dup-num-file</code>. <a href="https://github.com/shenwei356/seqkit/issues/436">#436</a></li>
</ul>
</li>
<li><code>seqkit stats</code>:<ul>
<li>New flag <code>-S/--skip-file-check</code> to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.</li>
</ul>
</li>
</ul>
</li>
<li><a href="https://github.com/shenwei356/seqkit/releases/tag/v2.6.1">SeqKit v2.6.1</a> - 2023-11-18
<a href="https://github.com/shenwei356/seqkit/releases/tag/v2.6.1"><img alt="Github Releases (by Release)" src="https://img.shields.io/github/downloads/shenwei356/seqkit/v2.6.1/total.svg" /></a><ul>
<li><code>seqkit</code>:<ul>
Expand Down
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