Multiple BAM files (ccs) input with Lima (PacBio)

Question

[aa9gj]

Hello, I am trying to input multiple bam files as input for Lima (multiple runs) but I don't see anywhere in the documentation on whether this is even feasible. Has anyone tried it before? currently, my plan is to run each sample separately and then merging with samtools at the end, is this okay?

Answer 1

[aa9gj]

I am responding to myself here in case anybody stumbles upon the same issue I was facing. I got a response from the maintainer on github

Lima has been developed with one input at a time. Maybe it's possible to use a dataset.xml, wrapping multiple input BAM files, but I recommend running it sample by sample and then merge.

People should stick to my plan if they are trying to use Lima on multiple cells. Make sure you sort after merging with samtools.

Good luck!