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Published 20 hours ago • verified publisher icon rjpbonnal

Shift to Trimmomatic

Open fstrozzi opened this issue 12 years ago • 2 comments

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.

fstrozzi avatar Jun 11 '12 09:06 fstrozzi

https://github.com/helios/bioruby-ngs/commit/9a45afb169ec7e1ddc726f0ee46ac59493994ea8

rjpbonnal avatar Jun 11 '12 09:06 rjpbonnal

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

rjpbonnal avatar Jun 11 '12 19:06 rjpbonnal