PBAlign for Quiver with pooled samples

[wbrashear]

I have assembled and circularized six BACs that were barcoded, pooled, and sequenced in a single PacBio movie following protocol outlined in the whitelisting (https://github.com/PacificBioscience...sting-Tutorial) and circularizing (https://github.com/PacificBioscience...g-and-trimming) tutorials.

I need to use pbalign to remap reads and produce the cmp.h5 file for Quiver correction. Is there a way to use only the subset of reads from the bax.h5 files that correspond to each BAC in pbalign (as done in the HGAP assembly process using the whitelist parameter)? Thanks for your help!

[rhall]

The whitelist parameter is usable across all protocols, for command line use

smrtpipe.py --examples

to find the directory of an example resequencing job, edit the xml to include the whitelist parameter in the same place as for HGAP and run the resequencing protocol. The circularized BACs will have to be imported as references, using

referenceUploader

command, or this can be done in SMRT Portal if you are using the GUI.