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bump CoverM to v0.7.0
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@AroneyS
AroneyS committed Jan 18, 2024
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4 changes: 2 additions & 2 deletions CITATION.cff
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Expand Up @@ -20,5 +20,5 @@ authors:
given-names: Ben J.
orcid: https://orcid.org/0000-0003-0670-7480
title: "CoverM: Read coverage calculator for metagenomics"
version: 0.6.1
date-released: 2021-02-25
version: 0.7.0
date-released: 2024-01-18
10 changes: 5 additions & 5 deletions Cargo.toml
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@@ -1,6 +1,6 @@
[package]
name = "coverm"
version = "0.6.1"
version = "0.7.0"
authors = ["Ben Woodcroft <[email protected]>"]
license = "GPL-3.0"
description = "Read coverage calculator for metagenomics"
Expand Down Expand Up @@ -28,10 +28,10 @@ lazy_static = "1.4.0"
rand = "0.8.*"
serde = "1.0"
version-compare = "0.1.0"
# bird_tool_utils = "0.3.0"
bird_tool_utils = { git = "https://github.com/wwood/bird_tool_utils" }
# galah = "0.3.0"
galah = { git = "https://github.com/wwood/galah" }
bird_tool_utils = "0.5.0"
# bird_tool_utils = { git = "https://github.com/wwood/bird_tool_utils" }
galah = "0.4.0"
# galah = { git = "https://github.com/wwood/galah" }
bird_tool_utils-man = "0.4.0"
roff = "0.2.*"
needletail = "0.5.*"
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40 changes: 27 additions & 13 deletions docs/coverm-cluster.html
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<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">
<html>

<head>

<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />

<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="author" content="Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology" />

Expand Down Expand Up @@ -63,7 +62,7 @@
<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">2021-02-25 (coverm 0.6.1)</span>
<span class="author_bio mbm">2024-01-18 (coverm 0.7.0)</span>
</div>
</div>
</div>
Expand All @@ -90,11 +89,11 @@
<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 0.6.1)</p>
<p>CoverM cluster - Cluster genome FASTA files by average nucleotide identity (version 0.7.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
<p><strong>coverm cluster</strong> &lt;GENOME_INPUTS&gt; &lt;OUTPUT_ARGUMENTS&gt;</p>
<p><strong>CoverM cluster</strong> &lt;GENOME_INPUTS&gt; &lt;OUTPUT_ARGUMENTS&gt;</p>
</div>
<div id="description" class="section level1">
<h1>DESCRIPTION</h1>
Expand All @@ -110,7 +109,7 @@ <h1>GENOME INPUT</h1>
</dl>
<!-- -->
<dl>
<dt><strong>-d</strong>, <strong>--genome-fasta-directory</strong> <em>PATH</em></dt>
<dt><strong>d</strong>, <strong>--genome-fasta-directory</strong> <em>PATH</em></dt>
<dd><p>Directory containing FASTA files of each genome.</p>
</dd>
</dl>
Expand All @@ -130,14 +129,20 @@ <h1>GENOME INPUT</h1>
<div id="filtering-parameters" class="section level1">
<h1>FILTERING PARAMETERS</h1>
<dl>
<dt><strong>--checkm2-quality-report</strong> <em>PATH</em></dt>
<dd><p>CheckM version 2 quality_report.tsv (i.e. the <code>quality_report.tsv</code> in the output directory output of <code>checkm2 predict ..</code>) for defining genome quality, which is used both for filtering and to rank genomes during clustering.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--checkm-tab-table</strong> <em>PATH</em></dt>
<dd><p>CheckM tab table (i.e. the output of <code>checkm .. --tab_table -f PATH ..</code>) for defining genome quality, which is used both for filtering and to rank genomes during clustering.</p>
<dd><p>CheckM tab table (i.e. the output of <code>checkm .. --tab_table -f PATH ..</code>). The information contained is used like <code>--checkm2-quality-report</code>.</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--genome-info</strong> <em>PATH</em></dt>
<dd><p>dRep style genome info table for defining quality. Used like <code>--checkm-tab-table</code>.</p>
<dd><p>dRep style genome info table for defining quality. The information contained is used like <code>--checkm2-quality-report</code>.</p>
</dd>
</dl>
<!-- -->
Expand All @@ -157,13 +162,13 @@ <h1>FILTERING PARAMETERS</h1>
<h1>CLUSTERING PARAMETERS</h1>
<dl>
<dt><strong>--ani</strong> <em>FLOAT</em></dt>
<dd><p>Overall ANI level to dereplicate at with FastANI. [default: <code>99</code>]</p>
<dd><p>Overall ANI level to dereplicate at with FastANI. [default: <code>95</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--min-aligned-fraction</strong> <em>FLOAT</em></dt>
<dd><p>Min aligned fraction of two genomes for clustering. [default: <code>50</code>]</p>
<dd><p>Min aligned fraction of two genomes for clustering. [default: <code>15</code>]</p>
</dd>
</dl>
<!-- -->
Expand Down Expand Up @@ -203,13 +208,19 @@ <h1>CLUSTERING PARAMETERS</h1>
</table>
<dl>
<dt><strong>--precluster-ani</strong> <em>FLOAT</em></dt>
<dd><p>Require at least this dashing-derived ANI for preclustering and to avoid FastANI on distant lineages within preclusters. [default: <code>95</code>]</p>
<dd><p>Require at least this dashing-derived ANI for preclustering and to avoid FastANI on distant lineages within preclusters. [default: <code>90</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--precluster-method</strong> <em>NAME</em></dt>
<dd><p>method of calculating rough ANI for dereplication. &#39;<code>dashing</code>&#39; for HyperLogLog, &#39;<code>finch</code>&#39; for finch MinHash. [default: <code>dashing</code>]</p>
<dd><p>method of calculating rough ANI for dereplication. &#39;<code>dashing</code>&#39; for HyperLogLog, &#39;<code>finch</code>&#39; for finch MinHash, &#39;<code>skani</code>&#39; for Skani. [default: <code>skani</code>]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--cluster-method</strong> <em>NAME</em></dt>
<dd><p>method of calculating ANI. &#39;<code>fastani</code>&#39; for FastANI, &#39;<code>skani</code>&#39; for Skani. [default: <code>skani</code>]</p>
</dd>
</dl>
</div>
Expand Down Expand Up @@ -311,6 +322,9 @@ <h1>AUTHOR</h1>



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54 changes: 41 additions & 13 deletions docs/coverm-contig.html
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<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">
<html>

<head>

<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />

<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="author" content="Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology" />

Expand Down Expand Up @@ -63,7 +62,7 @@
<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">2021-02-25 (coverm 0.6.1)</span>
<span class="author_bio mbm">2024-01-18 (coverm 0.7.0)</span>
</div>
</div>
</div>
Expand Down Expand Up @@ -95,7 +94,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm contig - Calculate read coverage per-contig (version 0.6.1)</p>
<p>coverm contig - Calculate read coverage per-contig (version 0.7.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand Down Expand Up @@ -149,7 +148,7 @@ <h1>READ MAPPING PARAMETERS</h1>
<h1>REFERENCE</h1>
<dl>
<dt><strong>-r</strong>, <strong>--reference</strong> <em>PATH</em></dt>
<dd><p>FASTA file of contigs e.g. concatenated genomes or metagenome assembly, or minimap2 index (with <code>--minimap2-reference-is-index</code>), or BWA index stem (with <code>-p bwa-mem</code>). If multiple references FASTA files are provided and <code>--sharded</code> is specified, then reads will be mapped to references separately as sharded BAMs. [required unless <code>-b/--bam-files</code> is specified]</p>
<dd><p>FASTA file of contigs e.g. concatenated genomes or metagenome assembly, or minimap2 index (with <code>--minimap2-reference-is-index</code>), strobealign index (with <code>--strobealign-use-index</code>), or BWA index stem (with <code>-p bwa-mem/bwa-mem2</code>). If multiple references FASTA files are provided and <code>--sharded</code> is specified, then reads will be mapped to references separately as sharded BAMs. [required unless <code>-b/--bam-files</code> is specified]</p>
</dd>
</dl>
</div>
Expand Down Expand Up @@ -182,13 +181,21 @@ <h1>MAPPING ALGORITHM OPTIONS</h1>
<td align="left">bwa mem using default parameters</td>
</tr>
<tr class="odd">
<td align="left"><code>bwa-mem2</code></td>
<td align="left">bwa-mem2 using default parameters</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-ont</code></td>
<td align="left">minimap2 with &#39;<code>-x map-ont</code>&#39; option</td>
</tr>
<tr class="even">
<tr class="odd">
<td align="left"><code>minimap2-pb</code></td>
<td align="left">minimap2 with &#39;<code>-x map-pb</code>&#39; option</td>
</tr>
<tr class="even">
<td align="left"><code>minimap2-hifi</code></td>
<td align="left">minimap2 with &#39;<code>-x map-hifi</code>&#39; option</td>
</tr>
<tr class="odd">
<td align="left"><code>minimap2-no-preset</code></td>
<td align="left">minimap2 with no &#39;<code>-x</code>&#39; option</td>
Expand All @@ -209,7 +216,19 @@ <h1>MAPPING ALGORITHM OPTIONS</h1>
<!-- -->
<dl>
<dt><strong>--bwa-params</strong> <em>PARAMS</em></dt>
<dd><p>Extra parameters to provide to BWA. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]</p>
<dd><p>Extra parameters to provide to BWA or BWA-MEM2. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--strobealign-params</strong> <em>PARAMS</em></dt>
<dd><p>Extra parameters to provide to strobealign. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--strobealign-use-index</strong></dt>
<dd><p>Use a pregenerated index (one that has been created with &#39;strobealign --create-index&#39;). The --reference option should be specified as the original FASTA file i.e. &#39;ref.fna&#39; not &#39;ref.fna.r100.sti&#39; [default: not set]</p>
</dd>
</dl>
</div>
Expand Down Expand Up @@ -262,6 +281,12 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<dd><p>Exclude supplementary alignments. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--include-secondary</strong></dt>
<dd><p>Include secondary alignments. [default: not set]</p>
</dd>
</dl>
</div>
<div id="coverage-calculation-options" class="section level1">
<h1>COVERAGE CALCULATION OPTIONS</h1>
Expand Down Expand Up @@ -301,7 +326,7 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
</tr>
<tr class="odd">
<td align="left"><code>count</code></td>
<td align="left">Number of reads aligned toq each contig. Note that a single read may be aligned to multiple contigs with supplementary alignments</td>
<td align="left">Number of reads aligned to each contig. Note that supplementary alignments are not counted.</td>
</tr>
<tr class="even">
<td align="left"><code>metabat</code></td>
Expand All @@ -323,7 +348,7 @@ <h1>COVERAGE CALCULATION OPTIONS</h1>
</table>
<dl>
<dt><strong>--min-covered-fraction</strong> <em>FRACTION</em></dt>
<dd><p>Genomes with less coverage than this reported as having zero coverage. [default: <code>10</code>]</p>
<dd><p>Contigs with less covered bases than this are reported as having zero coverage. [default: <code>0</code>]</p>
</dd>
</dl>
<!-- -->
Expand All @@ -348,7 +373,7 @@ <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>
<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>
Expand All @@ -367,7 +392,7 @@ <h1>OUTPUT</h1>
<!-- -->
<dl>
<dt><strong>--bam-file-cache-directory</strong> <em>DIRECTORY</em></dt>
<dd><p>Output BAM files generated during alignment to this directory. The directory may or may not exist. [default: not used]</p>
<dd><p>Output BAM files generated during alignment to this directory. The directory may or may not exist. Note that BAM files in this directory contain all mappings, including those that later are excluded by alignment thresholding (e.g. --min-read-percent-identity) or genome-wise thresholding (e.g. --min-covered-fraction). [default: not used]</p>
</dd>
</dl>
<!-- -->
Expand Down Expand Up @@ -418,7 +443,7 @@ <h1>GENERAL OPTIONS</h1>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</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>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
<p><strong>For thresholding arguments e.g. \-\-dereplication\-ani and \-\-min\-read\-percent\-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
Expand Down Expand Up @@ -465,6 +490,9 @@ <h1>AUTHOR</h1>



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22 changes: 15 additions & 7 deletions docs/coverm-filter.html
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<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">
<html>

<head>

<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />

<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="viewport" content="width=device-width, initial-scale=1" />

<meta name="author" content="Ben Woodcroft, Centre for Microbiome Research, Queensland University of Technology" />

Expand Down Expand Up @@ -63,7 +62,7 @@
<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">2021-02-25 (coverm 0.6.1)</span>
<span class="author_bio mbm">2024-01-18 (coverm 0.7.0)</span>
</div>
</div>
</div>
Expand All @@ -90,7 +89,7 @@
<article class="post-content">
<div id="name" class="section level1">
<h1>NAME</h1>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.6.1)</p>
<p>coverm filter - Threshold alignments with insufficient identity (version 0.7.0)</p>
</div>
<div id="synopsis" class="section level1">
<h1>SYNOPSIS</h1>
Expand All @@ -104,7 +103,7 @@ <h1>DESCRIPTION</h1>
<h1>FLAGS</h1>
<dl>
<dt><strong>--inverse</strong></dt>
<dd><p>Only keep reads which are unmapped or align below thresholds. Note that output records may still be marked as mapped if they do not meet the thresholds. [default: not set]</p>
<dd><p>Only keep reads which are unmapped or align below thresholds. Note that output records may still be marked as mapped if they do not meet the thresholds. When used with --proper-pairs, only proper pairs which fail alignment thresholds are output i.e. it does not &quot;invert&quot; the proper pairs flag. [default: not set]</p>
</dd>
</dl>
<!-- -->
Expand Down Expand Up @@ -207,11 +206,17 @@ <h1>ALIGNMENT THRESHOLDING</h1>
<dd><p>Exclude supplementary alignments. [default: not set]</p>
</dd>
</dl>
<!-- -->
<dl>
<dt><strong>--include-secondary</strong></dt>
<dd><p>Include secondary alignments. [default: not set]</p>
</dd>
</dl>
</div>
<div id="frequently-asked-questions-faq" class="section level1">
<h1>FREQUENTLY ASKED QUESTIONS (FAQ)</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>
<p><strong>For thresholding arguments e.g. --dereplication-ani and --min-read-percent-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
<p><strong>For thresholding arguments e.g. \-\-dereplication\-ani and \-\-min\-read\-percent\-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified?</strong> Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.</p>
</div>
<div id="exit-status" class="section level1">
<h1>EXIT STATUS</h1>
Expand Down Expand Up @@ -258,6 +263,9 @@ <h1>AUTHOR</h1>



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