Question: How to generate bam files for Quiver
gravatar for Biomonika (Noolean)
5.0 years ago by
State College, PA, USA
Biomonika (Noolean)3.1k wrote:

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
pacbio quiver • 2.0k views
ADD COMMENTlink written 5.0 years ago by Biomonika (Noolean)3.1k

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.

ADD REPLYlink written 5.0 years ago by h.mon30k
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