bcbio-nextgen

.. image:: artwork/github.png :alt: bcbio banner :align: center

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.

.. image:: https://travis-ci.org/bcbio/bcbio-nextgen.png :target: https://travis-ci.org/bcbio/bcbio-nextgen

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_.

.. _IPython parallel: http://ipython.org/ipython-doc/dev/index.html .. _parallel documentation: https://bcbio-nextgen.readthedocs.org/en/latest/contents/parallel.html .. _A single installer script: https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#automated .. _users page: https://bcbio-nextgen.readthedocs.org/en/latest/contents/introduction.html#users .. _developer documentation: https://bcbio-nextgen.readthedocs.org/en/latest/contents/code.html .. _variant calling, RNA-seq and small RNA pipelines: https://bcbio-nextgen.readthedocs.org/en/latest/contents/pipelines.html .. _parallel analysis and scaling: http://bcb.io/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/ .. _Automated validation: http://bcb.io/2014/05/12/wgs-trio-variant-evaluation/

Quick start

1. Install_ bcbio-nextgen with 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 bowtie2
   

   producing an editable system configuration file_ referencing the installed software, data and system information.

2. 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_.

3. Run analysis, distributed across 8 local cores::

     cd project1/work
     bcbio_nextgen.py ../config/project1.yaml -n 8
   

.. _system configuration file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_system.yaml .. _sample description file: https://github.com/bcbio/bcbio-nextgen/blob/master/config/bcbio_sample.yaml .. _Automatically create a processing description: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html#automated-sample-configuration .. _Install: https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#automated .. _configuration options: https://bcbio-nextgen.readthedocs.org/en/latest/contents/configuration.html

Documentation

See the full documentation_ and longer analysis-based articles <http://bcb.io>. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list_.

.. _full documentation: https://bcbio-nextgen.readthedocs.org .. _GitHub: https://github.com/bcbio/bcbio-nextgen/issues .. _biovalidation mailing list: https://groups.google.com/d/forum/biovalidation

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 <http://www.simonsfoundation.org/about-us/staff/staff-bios/#nick-carriero-ph-d>_, Simons Foundation
• Brad Chapman_, Harvard Chan Bioinformatics Core
• Saket Choudhary_, University Of Southern California
• Peter Cock_, The James Hutton Institute
• Matthias De Smet <https://github.com/matthdsm>_, Center for Medical Genetics, Ghent University Hospital, Belgium
• Matt Edwards_, MIT
• Mario Giovacchini_, Science for Life Laboratory, Stockholm
• Karl Gutwin <https://twitter.com/kgutwin>_, Biogen
• Jeff Hammerbacher_, Icahn School of Medicine at Mount Sinai
• Oliver Hofmann <https://umccr.github.io/>_, University of Melbourne Centre for Cancer Research
• John Kern <https://github.com/kern3020>_
• Rory Kirchner_, Harvard Chan Bioinformatics Core
• Tetiana Khotiainsteva <https://github.com/tetianakh>_, Ardigen
• Jakub Nowacki_, AstraZeneca
• John Morrissey <https://github.com/jwm>_, Harvard Chan Bioinformatics Core
• Lorena Pantano <https://github.com/lpantano>_, 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

.. _Miika Ahdesmaki: https://github.com/mjafin .. _Luca Beltrame: https://github.com/lbeltrame .. _Christian Brueffer: https://github.com/cbrueffer .. _Guillermo Carrasco: https://github.com/guillermo-carrasco .. _Alla Bushoy: https://github.com/abushoy .. _Brad Chapman: https://github.com/chapmanb .. _Peter Cock: https://github.com/peterjc .. _Mario Giovacchini: https://github.com/mariogiov .. _Rory Kirchner: https://github.com/roryk .. _Jakub Nowacki: https://github.com/jsnowacki .. _Brent Pedersen: https://github.com/brentp .. _James Porter: https://github.com/porterjamesj .. _Valentine Svensson: https://github.com/vals .. _Paul Tang: https://github.com/tanglingfung .. _Stephen Turner: https://github.com/stephenturner .. _Roman Valls: https://github.com/brainstorm .. _Kevin Ying: https://github.com/kevyin .. _Jeff Hammerbacher: https://github.com/hammer .. _Matt Edwards: https://github.com/matted .. _Saket Choudhary: https://github.com/saketkc .. _Vlad Saveliev: https://github.com/vladsaveliev

License

The code is freely available under the MIT license_.

.. _MIT license: http://www.opensource.org/licenses/mit-license.html