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lh3 / fermi-lite

Standalone C library for assembling Illumina short reads in small regions
MIT License
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Fermi-lite aggressive trimming #15

Open cgroza opened 4 years ago

cgroza commented 4 years ago

Hi, When setting aggressive trimming in fermi-lite to pop bubbles in heterozygous regions, what is the strategy being employed. Is the longer path in the bubble being kept or the shorter path? Or the one with highest average coverage? I am using fermi-lite to do local assembly of ~2kb regions.

Thanks, Cristian

lh3 commented 4 years ago

Fermi-lite chooses the path with more reads.