The GenomicConsensus package provides the quiver tool, PacBio's flagship consensus and variant caller. The backend logic is provided by the ConsensusCore and ConsensusCore2 libraries, which you must install first.

Make sure you have set up and activated your virtualenv, and installed pbcore, ConsensusCore, and ConsensusCore2 (which cannot be installed automatically by pip or setuptools at this time). Then:

% python setup.py install

Basic usage is as follows:

% quiver aligned_reads{.cmp.h5, .bam, .fofn, or .xml}    \
>     -r reference{.fasta or .xml} -o variants.gff       \
>     -o consensus.fasta -o consensus.fastq

in this example we perform haploid consensus and variant calling on the mapped reads in the aligned_reads.bam which was aligned to reference.fasta. The reference.fasta is only used for designating variant calls, not for computing the consensus. The consensus quality score for every position can be found in the output FASTQ file.

• More detailed installation instructions
• Quiver FAQ
• variants.gff spec
• CHANGELOG