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voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler
http://www.ncbi.nlm.nih.gov/pubmed/25609793
GNU General Public License v3.0
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Preset meta-large uses --min-count 1 #266

Open mdehollander opened 4 years ago

mdehollander commented 4 years ago

The preset meta-large uses the option --min-count 1, in contrast to the default --min-count 2: https://github.com/voutcn/megahit/blob/36f5d4543bddc887b26e6bd42d722c9aaefac10b/src/megahit#L500

This is not mentioned in the help message: https://github.com/voutcn/megahit/blob/36f5d4543bddc887b26e6bd42d722c9aaefac10b/src/megahit#L81

slambrechts commented 3 years ago

I also noticed this, and wonder why? Wouldn't complex metagenomes benefit from a higher --min-count setting? Or is this not as straightforward, because complex metagenomes might contain both organisms that are present at very high coverage and at low coverage?