DumbView: a PacBio genome browser for command-line nerds

Requirements: pbcore, GenomicConsensus

Install: python setup.py install

Use:

• View alignments to a window of the reference: dumbview aligned_reads.cmp.h5 [-r reference.fasta] -w<contigName>:<start>-<end>
• View alignments around all variant calls in a variants.gff file: dumbview variants.gff
• To enable "unaligned" mode (useful for eyeballing insertion variants) use -u

Notes:

• DumbView expects a FASTA index (.fai) file in the same directory as the reference FASTA. Make it with samtools faidx reference.fasta.
• Coordinates are 1-based, in agreement with the "GFF" convention and most other genome browsers.
• The consensus track shown at the bottom presently uses the Quiver "NoQVs" model, so it may not be the same consensus as you get from running Quiver. This will be fixed soon.

This is an unsupported tool and the code is horrendous. But I find it useful.

David Alexander, 2013