This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Demultiplex PacBio CCS reads on Mac

I have CCS reads from a PacBio Sequel platform (.bam, .fastq, .fasta files). My library was multiplexed. The same barcode (12 bp) is attached to both sides of the sequence (symmetric). To demultiplex, I know of Lima, but this only appears to work for linux. I have a Mac and would like to do everything on it (if possible).

Any help would be great. I suspect there may be a bamtools solution.

pacbio demultiplex next-gen sequencing
• 1,554 views • link
updated by lauraashaley • lauraashaley • written by manthony5955 • manthony5955

1 answer

If you have a Mac using the ARM architecture then that's going to be a big blocker. A lot of compiled software like lima will be designed to run in x86 architecture, not ARM.

Conda by default won't even show you packages which aren't compatible with your system. On an x86 system the below command finds numerous versions of lima, but running it on my MacBook it finds nothing:

conda search -c bioconda lima

If you want to do this on your Mac, one option could be to look into setting up a virtual machine which uses x86 architecture. However, depending on the type of analysis you're doing you still may find that your local machine is not powerful enough for this.

EDIT - I didn't notice when I answered that this question is 6 years old, I'm not sure the ARM issue was so relevant in 2020. I'll leave up this response nonetheless.

• 0 views • link
written by sholt6 • sholt6

Log in to answer this question.

More posts like this