How to generate bam files for Quiver

Question

[Biomonika (Noolean)]

I want to use Quiver as a standalone tool to polish my final assembly produced by different set of tools. What is recommended way to generate bam file that Quiver needs (maybe blasr, bwa mem)? Thanks.

quiver -j8 aligned_reads.bam \
  -r path/to/lambda.fasta \
  -o variants.gff -o consensus.fasta

[h.mon]

I didn't have the opportunity to work with PacBio data yet, but from what I've read, you should use pbalign, which is a wrapper around several tools which will generate alignments for Quiver.