options for linkage information or mapped reads?

[jvollme]

Since coverM is meant to replace bamm, are there any comparable options/workflows for getting contig-linkage information or to extract all reads that map to specific contigs?

[wwood]

Hi, good question. Not currently, I'm afraid. These features are not used so much around in my lab, I'm curious to know what your use case is actually.

Extracting all reads that map to a specific contig or set of contigs can be done with samtools view, I'm not sure of a solution to the linked reads question.

Thanks.

[apcamargo]

Just to put my two cents in, I think the main use case is to do a "pseudo-scaffolding" or to identify contigs that are linked to a set of contigs of interest (e.g.: contigs that comprise a MAG), extract all the reads that map to them and reassemble with the hopes of improving the MAG contiguity. I've done this before with pysam and it would be cool to have a tool that performs this faster and "less manually". I'm not sure if that's within CoverM's scope, though.