Blasr/Quiver - Best Practice for Current Versions?

[jpummil]

Basic workflow using the data you have and the latest versions of software installed using pitchfork:
bax.h5 -> bax2bam -> reads.bam
reads.bam + reference.fasta -> pbalign -> aligned_reads.bam
aligned_reads.bam -> variant_caller (quiver or arrow) -> consensus.fasta

Thanks so much, rhall! Just getting my data set up for a trial now ;-)

I'll update the thread when I'm done!

[rhall]

Basic workflow using the data you have and the latest versions of software installed using pitchfork:
bax.h5 -> bax2bam -> reads.bam
reads.bam + reference.fasta -> pbalign -> aligned_reads.bam
aligned_reads.bam -> variant_caller (quiver or arrow) -> consensus.fasta

[jpummil]

So, first time attempting to use quiver to polish an assembly I created in Canu. All of the software is installed and functional via command line (quiver, pbalign, bax2bam, quiver, arrow, etc). Our systems people installed using pitchfork.

I have the assembly in .fasta format and I also have 30ea bax.h5 files to utilize. The issue comes when I start looking at blasr which apparently no longer outputs cmp.h5 files that are preferred by pbalign. blasr now defaults to .bam files (nice for standardization I guess) and it isn't obvious that pbalign will utilize .bam as input. Found this little snippet which was somewhat informative:

https://github.com/PacificBiosciences/pbalign/wiki/Mapping-RS-II-reads-(in-movie.bax.h5)-and-calling-consensus-using-pbalign-BLASR-while--sam-option-is-deprecated

Ultimately, in short, I simply want to utilize the bax.h5 files with quiver (or arrow) to polish the assembly I did in Canu.