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Old 06-26-2013, 10:33 AM   #1
DrWorm
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Location: St. Louis, MO

Join Date: Apr 2013
Posts: 17
Default seq_crumbs memory issues

Hey all,

I've been loving the seq_crumbs package for trimming and filtering my Illumina data, and was excited to download the latest update that can handle paired end data. Unfortunately, when I tried to use the tools I noticed that the memory requirements had increased dramatically. I expected a modest increase in processing paired end data compared to single end files, but it was jumping from 8G for single end to 80G for pe. Has anyone else encountered this issue or am I doing something totally wrong?

Also, does anyone else know of tools for quality filtering and complexity filtering that maintain read pairs? I'm aware of trimmomatic and trim_galore for quality trimming, but I didn't think they do filtering based on the quality/complexity of the read overall.

Thanks!
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