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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
GNU General Public License v3.0
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--allow-outies by default ON #15

Open Arkadiy-Garber opened 4 years ago

Arkadiy-Garber commented 4 years ago

Hi!

I've been running flash2 that I installed via conda. There does not appear to be a way to turn off the --allow-outies option. Flash2 combines both in innie and outie orientations with and without this flag.

Thanks! Arkadiy

msettles commented 4 years ago

well depends on what you mean by innie/outie, its different from the original implementation of FLASH (where outies are reads from the mate-pair protocol) "our" outies are paired-end reads that produce complete overlaps, where the overhangs are adapter sequence and get trimmed off. So why would you want to turn that option off? WE may have hardcoded it on, and leave the param to maintain backwards compatibility. I don't recall. We've also moved on from Flash2 in favor of our new project HTStream https://github.com/s4hts/HTStream, which has hts_Overlapper