Question: Merging and then unmerging small contigs
gravatar for Philipp Bayer
3 months ago by
Philipp Bayer6.9k
Philipp Bayer6.9k wrote:

We've been using mosdepth a lot for coverage calculation of plant pangenomes but it starts to choke when you have many, many tiny contigs instead of a few large chromosomes because of the way the algorithm works.

I'm wondering - is there any tool which can take bam files of reads aligned to those contigs, then make a fake 'pseudomolecule' out of the contigs keeping in mind where each contig is located, then uses that to make a new bam file with the reads moved over to that fake pseudomolecule? That way I could run mosdepth much faster and then later change the resulting per-base coverage bed file back into the original contigs.

I'd write it myself but there are several chances to introduce off-by-one errors and I know I'll hit them all.

mosdepth bedtools • 224 views
ADD COMMENTlink written 3 months ago by Philipp Bayer6.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2718 users visited in the last hour