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dstreett / FLASH2

Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons
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flash for amplicons #12

Open pooranis opened 6 years ago

pooranis commented 6 years ago

Out of curiousity, the description says:

Flash2 has some improvements from flash_1 including new logic from innie and outie overlaps as well as some initial steps for flash for amplicons

I saw the modifications for innies and outies in the readme, but what are the "initial steps for flash for amplicons"?

Thanks.

msettles commented 6 years ago

Basically, adapters dimers are relatively common in amplicons. flash2 uses a big dumb rule of if 50% of a read is low quality (I think <Q10 by default) it discards the read. Thats what that means

pooranis commented 6 years ago

Thanks for the reply! I'm working on a pre-processing pipeline for amplicon data for the Nephele project: https://nephele.niaid.nih.gov/ And I'm doing some testing to include FLASH2 as part of it, so that's why I was curious.