Package: bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA
analysis. You write a high level configuration file specifying your inputs and
analysis parameters. This input drives a parallel run that handles distributed
execution, idempotent processing restarts and safe transactional steps. bcbio
provides a shared community resource that handles the data processing component
of sequencing analysis, providing researchers with more time to focus on the
downstream biology.FeaturesCommunity developed: We welcome contributors with the goal of
overcoming the biological, algorithmic and computational challenges
that face individual developers working on complex pipelines in
quickly changing research areas. See ourusers pagefor examples
of bcbio-nextgen deployments, and thedeveloper documentationfor
tips on contributing.Installation:A single installer scriptprepares all
third party software, data libraries and system configuration files.Automated validation: Compare variant calls against common reference
materials or sample specific SNP arrays to ensure call correctness.
Incorporation of multiple approaches for alignment, preparation and
variant calling enable unbiased comparisons of algorithms.Distributed: Focus onparallel analysis and scalingto handle
large population studies and whole genome analysis. Runs on single
multicore computers, in compute clusters usingIPython parallel,
or on the Amazon cloud. See theparallel documentationfor full
details.Multiple analysis algorithms: bcbio-nextgen provides configurablevariant calling, RNA-seq and small RNA pipelines.Quick startInstallbcbio-nextgenwith all tool dependencies and data files:wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \
  --genomes GRCh37 --aligners bwa --aligners bowtie2producing an editablesystem configuration filereferencing the installed
software, data and system information.Automatically create a processing descriptionof sample FASTQ and BAM files
from your project, and a CSV file of sample metadata:bcbio_nextgen.py -w template freebayes-variant project1.csv sample1.bam sample2_1.fq sample2_2.fqThis produces asample description filecontaining pipelineconfiguration options.Run analysis, distributed across 8 local cores:cd project1/work
bcbio_nextgen.py ../config/project1.yaml -n 8DocumentationSee thefull documentationandlonger analysis-based articles. We welcome enhancements or problem reports usingGitHuband discussion on thebiovalidation mailing list.ContributorsMiika Ahdesmaki, AstraZenecaLuca Beltrame, IRCCS “Mario Negri” Institute for Pharmacological Research, Milan, ItalyChristian Brueffer, Lund University, Lund, SwedenAlla Bushoy, AstraZenecaGuillermo Carrasco, Science for Life Laboratory, StockholmNick Carriero, Simons FoundationBrad Chapman, Harvard Chan Bioinformatics CoreSaket Choudhary, University Of Southern CaliforniaPeter Cock, The James Hutton InstituteMatthias De Smet, Center for Medical Genetics, Ghent University Hospital, BelgiumMatt Edwards, MITMario Giovacchini, Science for Life Laboratory, StockholmKarl Gutwin, BiogenJeff Hammerbacher, Icahn School of Medicine at Mount SinaiOliver Hofmann, University of Melbourne Centre for Cancer ResearchJohn KernRory Kirchner, Harvard Chan Bioinformatics CoreTetiana Khotiainsteva, ArdigenJakub Nowacki, AstraZenecaJohn Morrissey, Harvard Chan Bioinformatics CoreLorena Pantano, Harvard Chan Bioinformatics CoreBrent Pedersen, University of Colorado DenverJames Porter, The University of ChicagoValentine Svensson, Science for Life Laboratory, StockholmPaul Tang, UCSFStephen Turner, University of VirginiaRoman Valls, Science for Life Laboratory, StockholmKevin Ying, Garvan Institute of Medical Research, Sydney, AustraliaVlad Saveliev, Center for Algorithmic Biotechnology, St. Petersburg UniversityLicenseThe code is freely available under theMIT license.