PacBio® variant and consensus caller
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README.md

GenomicConsensus

Genome polishing and variant calling.


The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.

Availability

Latest version can be installed via bioconda package genomicconsensus.

Please refer to our official pbbioconda page for information on Installation, Support, License, Copyright, and Disclaimer.

Background on Quiver and Arrow

Quiver is the legacy consensus model based on a conditional random field approach. Quiver enables consensus accuracies on genome assemblies at accuracies approaching or even exceeding Q60 (one error per million bases). If you use the HGAP assembly protocol in SMRTportal 2.0 or later, Quiver runs automatically as the final "assembly polishing" step.

Over the years Quiver has proven difficult to train and develop, so we are phasing it out in favor of the new model, Arrow. Arrow is an improved consensus model based on a more straightforward hidden Markov model approach.

Quiver is supported for PacBio RS data. Arrow is supported for PacBio Sequel data and RS data with the P6-C4 chemistry.

Running


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

quiver is a shortcut for variantCaller --algorithm=quiver. Naturally, to use arrow you could use the arrow shortcut or variantCaller --algorithm=arrow.

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.

Note that 2.3 SMRTanalysis does not support "dataset" input (FOFN or XML files); those who need this feature should wait for the forthcoming release of SMRTanalysis 3.0 or build from GitHub sources.

More documentation

DISCLAIMER

THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.