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Shift to Trimmomatic #36

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fstrozzi opened this issue Jun 11, 2012 · 2 comments
Open

Shift to Trimmomatic #36

fstrozzi opened this issue Jun 11, 2012 · 2 comments
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@fstrozzi
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Considering removing FastX and using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic) to perform reads trimming based on quality values. Trimmomatic is written in Java, it's multithreaded and keeps the correct pairing during the trimming, if one of the two mates is lost due to low quality scores.
@ghost ghost assigned fstrozzi Jun 11, 2012
@rjpbonnal
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9a45afb

@rjpbonnal
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Trimmomatic can not handle concatenated gzip files. It is not a trimmomatic fault but it comes from Java, the bug still active http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4691425 but there is a workaround

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