explanation of GFA output

[lfaino]

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]

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