Trimming MiSeq data

[akjones]

Hello all,

Suggestions for any open source software for trimming/cleaning MiSeq data? I was thinking of giving Cutadapt a try but I would like to know what others have had success with.


Thanks

~Ana

[GenoMax]

Many on this forum depend on Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic

There are obviously other options.

Prinseq: http://prinseq.sourceforge.net/
Trim Galore: http://www.bioinformatics.babraham.a...s/trim_galore/

[mgogol]

If you don't need something terribly sophisticated, you could try fastx toolkit, but it's a bit of a blunter tool than trimmomatic. Nicer syntax, though, IMHO.