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annotate README @ 4:3d690162d629 draft

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Added more details for the required dependencies.
author Joachim Jacob <joachim.jacob@gmail.com>
date Wed, 20 Mar 2013 09:35:07 +0100
parents 934cd08c77af
children f6ffb9aa409e
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1 qualimap - 1.0.1
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2 =====================================================================
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3 <joachim.jacob@vib.be>
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4
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5 SUMMARY
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6 -------
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7 Qualimap examines sequencing alignment data in SAM/BAM files and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.
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8
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9 http://qualimap.bioinfo.cipf.es/
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10
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11 Garcia-Alcalde et.al, (2012) Qualimap: evaluating next generation sequencing aligmnent data,
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12 Bioinformatics. doi: 10.1093/bioinformatics/bts503
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13
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14 REQUIREMENTS AND INSTALLATION
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15 -----------------------------
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16 Install this tool in your Galaxy via the Toolshed
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18 ) Required dependencies:
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19 - Qualimap available in the PATH
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20 - Perl
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21 - Perl core module File::Temp and File::Basename
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22 - Perl module Log::Log4perl
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24 ) Integration into Galaxy
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25 Please use the toolshed
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26
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27 DETAILS AND ISSUES
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28 ------------------
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29 ) Qualimap suite provide various quality control tools to apply
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30 after mapping. Only bamqc is provided in this first version
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31 ) bamqc reports various statistics of an alignment.
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33 =====================================================================