explanation of GFA output

lh3 / miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

MIT License

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explanation of GFA output #58

Open lfaino opened 5 years ago

lfaino commented 5 years ago

Dear Developer, I would like to know if there is a meaning behind the "l" or "c" at the end of a contig name. I see that a conting with "c" is taking long time to finish the nanopolish process.

Thanks in advance Luigi

jts commented 5 years ago

Hi,

"c" means the contig is circular. If this is a plasmid or other extrachromosomal element it might have very high depth, which will take nanopolish a long time to process. You may want to downsample the data to ~100-200x.

Jared