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<chapter id="chap_specialparams">
  <chapterinfo>
    <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="versionfile"/>
    <author>
      <firstname>Bastien</firstname>
      <surname>Chevreux</surname>
      <email>bach@chevreux.org</email>
    </author>
    <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="copyrightfile"/>
  </chapterinfo>
  <blockquote>
    <attribution>Solomon Short</attribution>
    <para>
      <emphasis><quote>... .
      </quote></emphasis>
    </para>
  </blockquote>
  <title>Parameters for special situations</title>
  <sect1 id="sect_sp_introduction">
    <title>
      Introduction
    </title>
    <para>
      Most of this chapter and many sections are just stubs at the moment.
    </para>
  </sect1>
  <sect1 id="sect_sp_pacbio">
    <title>
      PacBio
    </title>
    <sect2 id="sect_sp_pacbio_ccs">
      <title>
	PacBio CCS reads
      </title>
      <para>
	Declare the sequencing technology to be high-quality PacBio (<emphasis
	role="bold">PCBIOHQ</emphasis>). The last time I worked with CCS, the
	ends of the reads were not really clean, so using the proposed end
	clipping (which needs to be manually switched on for PCBIOHQ reads)
	may be advisable.
      </para>
      <screen><userinput>...
parameters = PCBIOHQ_SETTINGS -CL:pec=yes
...

readgroup
technology=pcbiohq
data=...
...</userinput></screen>
    </sect2>
    <sect2 id="sect_sp_pacbio_ec">
      <title>
	PacBio error corrected reads
      </title>
      <para>
	Declare the sequencing technology to be high-quality PacBio (<emphasis
	role="bold">PCBIOHQ</emphasis>). For self-corrected data or data
	corrected with other sequencing technologies, it is recommended to
	change the <arg>-CO:mrpg</arg> setting to a value which is 1/4th to
	1/5th of the average coverage of the corrected PacBio reads across the
	genome. E.g.:
      </para>
      <screen><userinput>...
parameters = PCBIOHQ_SETTINGS -CO:mrpg=5
...

readgroup
technology=pcbiohq
data=...
...</userinput></screen>
      <para>
	for a project which has ~24x coverage. This necessity may change in
	later versions of MIRA though.
      </para>
    </sect2>
  </sect1>
</chapter>
