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How to generate bam files for Quiver

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
quiver pacbio
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updated by Ram Ram • written by Biomonika (Noolean) Biomonika (Noolean)

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.

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written by h.mon h.mon

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