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v0.6.0
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wwood committed Dec 10, 2020
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2 changes: 1 addition & 1 deletion Cargo.toml
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[package]
name = "coverm"
version = "0.5.0"
version = "0.6.0"
authors = ["Ben Woodcroft <benjwoodcroft@gmail.com>"]
license = "GPL-3.0"
description = "Read coverage calculator for metagenomics"
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4 changes: 2 additions & 2 deletions docs/coverm-cluster.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm cluster usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-08-28 (coverm 0.5.0)</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
</div>
</div>
</div>
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<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.5.0)</p>
<p>coverm cluster - Cluster genome FASTA files by average nucleotide identity (version 0.6.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
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33 changes: 30 additions & 3 deletions docs/coverm-contig.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm contig usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-08-28 (coverm 0.5.0)</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
</div>
</div>
</div>
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<li><a href="#coverage-calculation-options">COVERAGE CALCULATION OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
</div>
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<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm contig - Calculate read coverage per-contig (version 0.5.0)</p>
<p>coverm contig - Calculate read coverage per-contig (version 0.6.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -313,6 +315,10 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<td align="left"><code>rpkm</code></td>
<td align="left">Reads mapped per kilobase of contig, per million mapped reads</td>
</tr>
<tr class="odd">
<td align="left"><code>tpm</code></td>
<td align="left">Transcripts Per Million as described in Li et al 2010 <a href="https://doi.org/10.1093/bioinformatics/btp692" class="uri">https://doi.org/10.1093/bioinformatics/btp692</a></td>
</tr>
</tbody>
</table>
<dl>
Expand Down Expand Up @@ -342,6 +348,12 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<div id="output" class="section level1">
<h1>OUTPUT</h1>
<dl>
<dt><strong>o</strong>, <strong>--output-file</strong> <em>FILE</em></dt>
<dd><p>Output coverage values to this file, or &#39;-&#39; for STDOUT. [default: output to STDOUT]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--output-format</strong> <em>FORMAT</em></dt>
<dd><p>Shape of output: &#39;sparse&#39; for long format, &#39;dense&#39; for species-by-site. [default: dense]</p>
</dd>
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</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
<dl>
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</dd>
</dl>
</div>
<div id="examples" class="section level1">
<h1>EXAMPLES</h1>
<dl>
<dt>Calculate mean coverage from reads and assembly</dt>
<dd><p><strong>$ coverm contig --coupled read1.fastq.gz read2.fastq.gz --reference assembly.fna</strong></p>
</dd>
<dt>Calculate MetaBAT adjusted coverage from a sorted BAM file, saving the unfiltered BAM files in the saved_bam_files folder</dt>
<dd><p><strong>$ coverm contig --method metabat --bam-files my.bam --bam-file-cache-directory saved_bam_files</strong></p>
</dd>
</dl>
</div>
<div id="author" class="section level1">
<h1>AUTHOR</h1>
<blockquote>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
</blockquote>
</div>
</article>
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23 changes: 20 additions & 3 deletions docs/coverm-filter.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm filter usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-08-28 (coverm 0.5.0)</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
</div>
</div>
</div>
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<li><a href="#flags">FLAGS</a></li>
<li><a href="#options">OPTIONS</a></li>
<li><a href="#alignment-thresholding">ALIGNMENT THRESHOLDING</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
</div>
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<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.5.0)</p>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.6.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -206,6 +208,10 @@ <h1>ALIGNMENT THRESHOLDING</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
<dl>
Expand All @@ -226,10 +232,21 @@ <h1>EXIT STATUS</h1>
</dd>
</dl>
</div>
<div id="examples" class="section level1">
<h1>EXAMPLES</h1>
<dl>
<dt>Filter a BAM file by removing alignments shorter than 50bp</dt>
<dd><p><strong>$ coverm filter --bam-files input.bam --output-bam filtered.bam --min-read-aligned-length 50</strong></p>
</dd>
<dt>Filter inverse: Keep alignments that have &lt;95% alignment identity and those which do map at all. Note that the output BAM file will likely records that are still mapped, but align with &lt; 95% identity. Use 16 threads for output compression</dt>
<dd><p><strong>$ coverm filter -b input.bam -o inverse_filtered.bam --inverse --min-read-percent-identity 0.95 --threads 16</strong></p>
</dd>
</dl>
</div>
<div id="author" class="section level1">
<h1>AUTHOR</h1>
<blockquote>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
</blockquote>
</div>
</article>
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36 changes: 33 additions & 3 deletions docs/coverm-genome.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm genome usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-08-28 (coverm 0.5.0)</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
</div>
</div>
</div>
Expand All @@ -85,7 +85,9 @@
<li><a href="#coverage-calculation-options">COVERAGE CALCULATION OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
</div>
Expand All @@ -94,7 +96,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm genome - Calculate read coverage per-genome (version 0.5.0)</p>
<p>coverm genome - Calculate read coverage per-genome (version 0.6.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -476,6 +478,10 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<td align="left"><code>rpkm</code></td>
<td align="left">Reads mapped per kilobase of genome, per million mapped reads</td>
</tr>
<tr class="odd">
<td align="left"><code>tpm</code></td>
<td align="left">Transcripts Per Million as described in Li et al 2010 <a href="https://doi.org/10.1093/bioinformatics/btp692" class="uri">https://doi.org/10.1093/bioinformatics/btp692</a></td>
</tr>
</tbody>
</table>
<dl>
Expand Down Expand Up @@ -505,6 +511,12 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
<div id="output" class="section level1">
<h1>OUTPUT</h1>
<dl>
<dt><strong>o</strong>, <strong>--output-file</strong> <em>FILE</em></dt>
<dd><p>Output coverage values to this file, or &#39;-&#39; for STDOUT. [default: output to STDOUT]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--output-format</strong> <em>FORMAT</em></dt>
<dd><p>Shape of output: &#39;sparse&#39; for long format, &#39;dense&#39; for species-by-site. [default: <code>dense</code>]</p>
</dd>
Expand Down Expand Up @@ -566,6 +578,10 @@ <h1>GENERAL OPTIONS</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
<dl>
Expand All @@ -586,10 +602,24 @@ <h1>EXIT STATUS</h1>
</dd>
</dl>
</div>
<div id="examples" class="section level1">
<h1>EXAMPLES</h1>
<dl>
<dt>Map paired reads to 2 genomes, and output relative abundances to output.tsv</dt>
<dd><p><strong>$ coverm genome --coupled read1.fastq.gz read2.fastq.gz --genome-fasta-files genome1.fna genome2.fna -o output.tsv</strong></p>
</dd>
<dt>Calculate coverage of genomes defined as .fna files in genomes_directory/ from a sorted BAM file</dt>
<dd><p><strong>$ coverm genome --bam-files my.bam --genome-fasta-directory genomes_directory/</strong></p>
</dd>
<dt>Dereplicate genomes at 99% ANI before mapping unpaired reads</dt>
<dd><p><strong>$ coverm genome --genome-fasta-directory genomes/ --dereplicate --single single_reads.fq.gz</strong></p>
</dd>
</dl>
</div>
<div id="author" class="section level1">
<h1>AUTHOR</h1>
<blockquote>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
</blockquote>
</div>
</article>
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20 changes: 17 additions & 3 deletions docs/coverm-make.html
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<div class="cover-card table-cell table-middle">
<span class="author_name">coverm make usage</span>
<span class="author_bio mbm">Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology</span>
<span class="author_bio mbm">2020-08-28 (coverm 0.5.0)</span>
<span class="author_bio mbm">2020-12-11 (coverm 0.6.0)</span>
</div>
</div>
</div>
Expand All @@ -81,7 +81,9 @@
<li><a href="#mapping-algorithm-options">MAPPING ALGORITHM OPTIONS</a></li>
<li><a href="#output">OUTPUT</a></li>
<li><a href="#general-options">GENERAL OPTIONS</a></li>
<li><a href="#frequently-asked-questions">FREQUENTLY ASKED QUESTIONS</a></li>
<li><a href="#exit-status">EXIT STATUS</a></li>
<li><a href="#examples">EXAMPLES</a></li>
<li><a href="#author">AUTHOR</a></li>
</ul>
</div>
Expand All @@ -90,7 +92,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm make - Generate BAM files through mapping (version: 0.5.0)</p>
<p>coverm make - Generate BAM files through mapping (version: 0.6.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -244,6 +246,10 @@ <h1>GENERAL OPTIONS</h1>
</dd>
</dl>
</div>
<div id="frequently-asked-questions" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS</h1>
<p><strong>Can the temporary directory used be changed?</strong> CoverM makes use of the system temporary directory (often <code>/tmp</code>) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the <code>TMPDIR</code> environment variable e.g. to set it to use the current directory: <code>TMPDIR=. coverm genome &lt;etc&gt;</code></p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
<dl>
Expand All @@ -264,10 +270,18 @@ <h1>EXIT STATUS</h1>
</dd>
</dl>
</div>
<div id="examples" class="section level1">
<h1>EXAMPLES</h1>
<dl>
<dt>Map pair of read files to the combined_genomes.fna reference, storing sorted BAM files in output_dir/</dt>
<dd><p><strong>$ coverm make -r combined_genomes.fna -1 read1.fq -2 read2.fq -o output_dir</strong></p>
</dd>
</dl>
</div>
<div id="author" class="section level1">
<h1>AUTHOR</h1>
<blockquote>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
<pre><code>Ben J. Woodcroft, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology &lt;benjwoodcroft near gmail.com&gt;</code></pre>
</blockquote>
</div>
</article>
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