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faircloth-lab / illumiprocessor

pre-process illumina reads
http://illumiprocessor.readthedocs.org/
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Support for other trimmers #21

Open mkweskin opened 4 weeks ago

mkweskin commented 4 weeks ago

Hi @brantfaircloth, I'm considering forking and modifying Illumiprocessor to use other trimmers (trim galore, fastp). Is this a direction you're interested in illumiprocessor going? Are you open to pull requests?

On the NMNH HPC we've been using a version that was modified to use trim galore because java programs (trimmomatic) are memory hungry on our HPC. Also, fastp has become popular recently. I believe it does better at poly-G trimming which is needed for data produced by two-channel Illumina technology. Thanks

brantfaircloth commented 4 weeks ago

Hi Matt,

I'd be interested and definitely open to pull requests. I've actually been using cutadapt recently - it's vastly faster than Trimmomatic and pretty flexible for lots of different used. Although I haven't gotten around to it, my plan was to replace Trimmomatic with cutadapt, in terms of the tutorial.