QC metrics from pacbio long reads data

Question

[eli_bayat]

Hello,

I have two samples that were sequenced using pacbio technology. These samples are different in terms of their shearing methods. I also have SMRTLink installed through command line interface.

I want to run some primary analysis to compare these samples, for example coverage bias, alignment summary metrics, and any thing else that can help with understanding differences between these samples.

I have unaligned bam file, pbi and xml files for each sample. I looked into pacbio guid but I couldn't find anything that helps me with these metrics.

Is there any tool I can use within SMRTLink that can do these analysis?

Thanks

Answer 1

[gconcepcion]

You're looking for the Mapping Analysis application - cromwell.workflows.pb_align_ccs on page 103 of the SMRTLink 10.1 docs you linked.

Running pbcromwell run pb_align_ccs ... will allow you to run the GUI mapping analysis on the command line.

or pbcromwell run pb_align_subreads... if you have subread data.

You can also just use pbmm2 that's included w/ the SMRTlink install to do the mapping manually if you are so inclined. https://github.com/PacificBiosciences/pbmm2