kraken_tools

These scripts are designed to help Kraken users with downstream
analysis of Kraken results.

An all-encompassing R toolkit designed to streamline the
process of calling various bioinformatics software and then performing data
analysis and visualization in R. With 'blit', users can easily integrate a
wide array of bioinformatics command line tools into their workflows,
leveraging the power of R for sophisticated data manipulation and graphical
representation.

Yun Peng

blit

Bioinformatics Library for Integrated Tools

Shixiang Wang

Jennifer Lu

Li Song

X. Shirley Liu

kraken_tools function

<dl><dt>script</dt>
<dd>Name of the kraken2 script. One of
<code>"combine_kreports"</code>, <code>"combine_mpa"</code>, <code>"extract_kraken_reads"</code>, <code>"filter_bracken_out"</code>, <code>"fix_unmapped"</code>, <code>"kreport2krona"</code>, <code>"kreport2mpa"</code>, <code>"make_kreport"</code>, and <code>"make_ktaxonomy"</code>.</dd>
<dt>...</dt>
<dd>&lt;<a href="https://rlang.r-lib.org/reference/dyn-dots.html">dynamic dots</a>&gt; Additional arguments passed to <code>kraken_tools</code> command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using <code><a href="/link/shQuote()?package=blit&version=0.2.0" data-mini-rdoc="blit::shQuote()">shQuote()</a></code>. Details see: <code>cmd_help(kraken_tools())</code>.</dd>
<dt>python</dt>
<dd>A string of path to <code>python</code> command.</dd></dl>

Arguments

KrakenTools is a suite of scripts to be used alongside the Kraken,
KrakenUniq, Kraken 2, or Bracken programs. — kraken_tools

<dl>

<dt>script</dt>
<dd>Name of the kraken2 script. One of
<code>"combine_kreports"</code>, <code>"combine_mpa"</code>, <code>"extract_kraken_reads"</code>, <code>"filter_bracken_out"</code>, <code>"fix_unmapped"</code>, <code>"kreport2krona"</code>, <code>"kreport2mpa"</code>, <code>"make_kreport"</code>, and <code>"make_ktaxonomy"</code>.</dd>


<dt>...</dt>
<dd>&lt;<a href='https://rlang.r-lib.org/reference/dyn-dots.html'>dynamic dots</a>&gt; Additional arguments passed to <code>kraken_tools</code> command. Empty arguments are automatically trimmed. If a single argument, such as a file path, contains spaces, it must be quoted, for example using <code><a href='https://rdrr.io/r/base/shQuote.html'>shQuote()</a></code>. Details see: <code>cmd_help(kraken_tools())</code>.</dd>


<dt>python</dt>
<dd>A string of path to <code>python</code> command.</dd>

</dl>

kraken_tools: KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs.

Description

Usage

Value

Arguments

See Also