+Validated, scalable, community developed variant calling and RNA-seq 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-nextgen 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 and RNA-seq 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 at ReadTheDocs. 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 +
- 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 +
- Matt Edwards, MIT +
- Mario Giovacchini, Science for Life Laboratory, Stockholm +
- Karl Gutwin, Biogen +
- Jeff Hammerbacher, Icahn School of Medicine at Mount Sinai +
- John Kern +
- Rory Kirchner, Harvard Chan Bioinformatics Core +
- 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 +
- Roman Valls, Science for Life Laboratory, Stockholm +
- Kevin Ying, Garvan Institute of Medical Research, Sydney, Australia +
License
+The code is freely available under the MIT license.
+