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How can I parallelize on multiple servers?

You can parallelize by chunking. Since ccs v4.0.0, direct chunking via --chunk is possible. For this, the .subreads.bam file must accompanied by a .pbi file. To generate the index subreads.bam.pbi, use pbindex, which can be installed with conda install pbbam.

pbindex movie.subreads.bam

An example workflow, all ccs invocations can run simultaneously:

ccs movie.subreads.bam movie.ccs.1.bam --chunk 1/10 -j <THREADS>
ccs movie.subreads.bam movie.ccs.2.bam --chunk 2/10 -j <THREADS>
ccs movie.subreads.bam movie.ccs.10.bam --chunk 10/10 -j <THREADS>

Merge chunks with pbmerge and index with pbindex

pbmerge -o movie.ccs.bam movie.ccs.*.bam
pbindex movie.ccs.bam

or use samtools

samtools merge [email protected] movie.ccs.bam movie.ccs.*.bam