Best-practice pipelines for fully automated high throughput sequencing analysis
Project description
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.
Features
Community 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 our users page for examples of bcbio-nextgen deployments, and the developer documentation for tips on contributing.
Installation: A single installer script prepares 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 on parallel analysis and scaling to handle large population studies and whole genome analysis. Runs on single multicore computers, in compute clusters using IPython parallel, or on the Amazon cloud. See the parallel documentation for full details.
Multiple analysis algorithms: bcbio-nextgen provides configurable variant calling, RNA-seq and small RNA pipelines.
Quick start
Install bcbio-nextgen with all tool dependencies and data files:
wget https://raw.github.com/chapmanb/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 bowtie2
producing an editable system configuration file referencing the installed software, data and system information.
Automatically create a processing description of 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.fq
This produces a sample description file containing pipeline configuration options.
Run analysis, distributed across 8 local cores:
cd project1/work bcbio_nextgen.py ../config/project1.yaml -n 8
Documentation
See the full documentation and longer analysis-based articles. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list.
Contributors
Miika Ahdesmaki, AstraZeneca
Luca Beltrame, IRCCS “Mario Negri” Institute for Pharmacological Research, Milan, Italy
Christian Brueffer, Lund University, Lund, Sweden
Alla Bushoy, AstraZeneca
Guillermo Carrasco, Science for Life Laboratory, Stockholm
Nick Carriero, Simons Foundation
Brad Chapman, Harvard Chan Bioinformatics Core
Saket Choudhary, University Of Southern California
Peter Cock, The James Hutton Institute
Matthias De Smet, Center for Medical Genetics, Ghent University Hospital, Belgium
Matt Edwards, MIT
Mario Giovacchini, Science for Life Laboratory, Stockholm
Karl Gutwin, Biogen
Jeff Hammerbacher, Icahn School of Medicine at Mount Sinai
Oliver Hofmann, Wolfson Wohl Cancer Research Center
Rory Kirchner, Harvard Chan Bioinformatics Core
Tetiana Khotiainsteva, Ardigen
Jakub Nowacki, AstraZeneca
John Morrissey, Harvard Chan Bioinformatics Core
Lorena Pantano, Harvard Chan Bioinformatics Core
Brent Pedersen, University of Colorado Denver
James Porter, The University of Chicago
Valentine Svensson, Science for Life Laboratory, Stockholm
Paul Tang, UCSF
Stephen Turner, University of Virginia
Roman Valls, Science for Life Laboratory, Stockholm
Kevin Ying, Garvan Institute of Medical Research, Sydney, Australia
Vlad Saveliev, Center for Algorithmic Biotechnology, St. Petersburg University
License
The code is freely available under the MIT license.
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