view tools/ilmn_pacbio/quake.xml @ 0:9071e359b9a3

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<tool id="quake" name="Quake" version="1.0.0">
  <description>Quality-aware error correction</description>
  <command interpreter="python">
    quake_wrapper.py --default_cutoff=10 --headers -k $k -f $fofnfile -p 12 > $output1
  </command>
  <inputs>
    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
  </inputs>
  <configfiles>
    <configfile name="fofnfile">
${input1.file_name}
    </configfile>
  </configfiles>
  <outputs>
    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
  </outputs>
  <help>

**What it does**

Applies the Quake_ algorithm for quality-aware correction of
substitution error in short reads.

Kelley DR, Schatz MC, Salzberg SL.
"Quake: quality-aware detection and correction of sequencing errors."
*Genome Biol.* 2010;11(11):R116.

.. _Quake: http://www.cbcb.umd.edu/software/quake

**Parameter list**

k
    k-mer size for detecting spurious k-mers versus true k-mers from
    the genome.  Recommendations for choosing a value of k can be found
    here_.

.. _here: http://www.cbcb.umd.edu/software/quake/faq.html

**Output**

A FASTQ file of corrected and trimmed reads.
  </help>
</tool>