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Updated docs.
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‎config.h.in

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/* Define to 1 if you have the <inttypes.h> header file. */
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#undef HAVE_INTTYPES_H
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/* Define to 1 if you have the `hts' library (-lhts). */
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/* Define to 1 if you have the 'hts' library (-lhts). */
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#undef HAVE_LIBHTS
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/* Define to 1 if you have the `pthread' library (-lpthread). */
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/* Define to 1 if you have the 'pthread' library (-lpthread). */
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#undef HAVE_LIBPTHREAD
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/* Define to 1 if you have the `z' library (-lz). */
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/* Define to 1 if you have the 'z' library (-lz). */
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/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
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/* Define to 1 if your system has a GNU libc compatible 'malloc' function, and
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to 0 otherwise. */
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/* Define to 1 if you have the `memmove' function. */
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/* Define to 1 if your system has a GNU libc compatible `realloc' function,
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/* Define to 1 if your system has a GNU libc compatible 'realloc' function,
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and to 0 otherwise. */
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/* Define to 1 if you have the <stdint.h> header file. */
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/* Define to 1 if you have the <stdio.h> header file. */
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/* Define to 1 if you have the <stdlib.h> header file. */
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#undef HAVE_STDLIB_H
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/* Define to 1 if you have the <unistd.h> header file. */
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/* Name of package */
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/* Define to the version of this package. */
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#undef PACKAGE_VERSION
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/* Define to 1 if you have the ANSI C header files. */
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/* Define to 1 if all of the C89 standard headers exist (not just the ones
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required in a freestanding environment). This macro is provided for
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backward compatibility; new code need not use it. */
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#define below would cause a syntax error. */
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‎docs/html/cookbookpage.html

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<head>
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<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
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<meta http-equiv="X-UA-Compatible" content="IE=9"/>
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<meta name="generator" content="Doxygen 1.9.5"/>
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<meta name="generator" content="Doxygen 1.10.0"/>
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<meta name="viewport" content="width=device-width, initial-scale=1"/>
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<meta name="description" content="iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files."/>
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<meta name="keywords" content="variants calling,consensus,htslib,primal,primer,trimming,amplicon sequencing,ivar"/>
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<link href="tabs.css" rel="stylesheet" type="text/css"/>
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<script type="text/javascript" src="jquery.js"></script>
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<script type="text/javascript" src="dynsections.js"></script>
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<script type="text/javascript" src="cookie.js"></script>
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<link href="search/search.css" rel="stylesheet" type="text/css"/>
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<script type="text/javascript" src="search/searchdata.js"></script>
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</table>
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</div>
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<!-- end header part -->
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<!-- Generated by Doxygen 1.9.5 -->
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<!-- Generated by Doxygen 1.10.0 -->
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<script type="text/javascript">
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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var searchBox = new SearchBox("searchBox", "search/",'.html');
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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$(function() {
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initMenu('',true,false,'search.php','Search');
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});
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/* @license-end */
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</script>
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</div><!-- top -->
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<div><div class="header">
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<div class="headertitle"><div class="title">Cookbook </div></div>
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<div class="headertitle"><div class="title">Cookbook</div></div>
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</div><!--header-->
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<div class="contents">
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<div class="textblock"><p ><a class="anchor" id="md_docs_COOKBOOK"></a></p>
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<p >Two pipelines to call iSNVs from known and unknown reference sequences have been written in <a href="https://snakemake.readthedocs.io/en/stable/">snakemake</a>.</p>
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<p >The two pipelines are distributed along with iVar and are present in the<a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">pipeline/</a> and <a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field">pipeline_field/</a> fodlers respectively.</p>
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<p >For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.</p>
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<div class="textblock"><p><a class="anchor" id="md_docs_2_c_o_o_k_b_o_o_k"></a></p>
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<p>Two pipelines to call iSNVs from known and unknown reference sequences have been written in <a href="https://snakemake.readthedocs.io/en/stable/">snakemake</a>.</p>
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<p>The two pipelines are distributed along with iVar and are present in the<a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">pipeline/</a> and <a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field">pipeline_field/</a> fodlers respectively.</p>
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<p>For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.</p>
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<div class="fragment"><div class="line">in_dir = &quot;&lt;input fastq files&gt;&quot;</div>
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<div class="line">out_dir = &quot;&lt;output directory&gt;&quot;</div>
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<div class="line">bed = &quot;&lt;bed-file-with-primer-positions&gt;&quot;</div>
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<div class="line">ref=&quot;&lt;path to reference fasta&gt;&quot;</div>
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</div><!-- fragment --><p ><img src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png" alt="" width="500" class="inline"/></p>
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</div><!-- fragment --><p><img src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png" alt="" width="500" class="inline"/></p>
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<h2>Call iSNVs from samples with known reference sequence</h2>
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<p ><a href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb">Link to Jupyter Notebook</a></p>
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<p ><a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">Link to pipeline</a></p>
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<p><a href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb">Link to Jupyter Notebook</a></p>
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<p><a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">Link to pipeline</a></p>
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<h3>Dependencies:</h3>
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<ul>
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<li><a href="https://github.com/andersen-lab/ivar">iVar</a></li>
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<li><a href="https://bedtools.readthedocs.io/en/latest/">bedtools</a></li>
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</ul>
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<h2>Call iSNVs from samples with unknown reference sequence</h2>
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<p ><a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field/">Link to pipeline</a></p>
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<p><a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field/">Link to pipeline</a></p>
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<h3>Dependencies:</h3>
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<ul>
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<li><a href="https://github.com/andersen-lab/ivar">iVar</a></li>
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<hr class="footer"/><address class="footer"><small>
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‎docs/html/dir_49e56c817e5e54854c35e136979f97ca.html

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<meta name="description" content="iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates. We implemented the following functions in iVar: (1) trimming of primers and low-quality bases, (2) consensus calling, (3) variant calling - both iSNVs and insertions/deletions, and (4) identifying mismatches to primer sequences and excluding the corresponding reads from alignment files."/>
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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/* @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&amp;dn=expat.txt MIT */
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