Question: Merging and then unmerging small contigs
1
gravatar for Philipp Bayer
13 days ago by
Philipp Bayer6.8k
Australia/Perth/UWA
Philipp Bayer6.8k 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 • 147 views
ADD COMMENTlink written 13 days ago by Philipp Bayer6.8k
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