bcbio-nextgen

Best-practice pipelines for fully automated high throughput sequencing analysis

Project description

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing 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. The goal is to provide 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
Brad Chapman, Harvard School of Public Health
Peter Cock, The James Hutton Institute
Mario Giovacchini, Science for Life Laboratory, Stockholm
Rory Kirchner, Harvard School of Public Health
Jakub Nowacki, AstraZeneca
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
Jeff Hammerbacher, Icahn School of Medicine at Mount Sinai
danielevo

License

The code is freely available under the MIT license.

Project details

Release history Release notifications | RSS feed

1.1.5

Apr 12, 2019

1.1.4

Apr 3, 2019

1.1.3

Jan 29, 2019

1.1.2

Dec 12, 2018

1.1.1

Nov 6, 2018

1.1.0

Jul 11, 2018

1.0.9

Apr 10, 2018

1.0.8

Feb 5, 2018

1.0.7

Jan 6, 2018

1.0.6

Nov 5, 2017

1.0.5

Sep 11, 2017

1.0.4

Jul 9, 2017

1.0.3

May 7, 2017

1.0.2

Mar 7, 2017

1.0.1

Jan 17, 2017

1.0.0

Nov 20, 2016

0.9.9

Jul 18, 2016

0.9.8

May 20, 2016

0.9.7

Mar 29, 2016

0.9.6

Feb 12, 2016

0.9.5

Dec 12, 2015

0.9.4

Oct 14, 2015

0.9.4a0 pre-release

Sep 28, 2015

0.9.3

Sep 27, 2015

0.9.2

Sep 1, 2015

0.9.1

Aug 6, 2015

0.9.0

Jun 20, 2015

0.8.9

May 10, 2015

0.8.8

Apr 29, 2015

0.8.7

Mar 10, 2015

0.8.6

Feb 23, 2015

0.8.5

Jan 11, 2015

0.8.4

Nov 29, 2014

0.8.3

Nov 19, 2014

0.8.2

Sep 17, 2014

0.8.1

Aug 29, 2014

This version

0.8.0

Jul 28, 2014

0.7.9

May 19, 2014

0.7.8

Mar 21, 2014

0.7.7

Feb 27, 2014

0.7.6

Jan 15, 2014

0.7.5

Nov 29, 2013

0.7.4

Oct 20, 2013

0.7.3

Sep 22, 2013

0.7.2

Aug 30, 2013

0.7.1

Aug 12, 2013

0.7.0

Jul 30, 2013

0.6.5

Jun 7, 2013

0.6.4

May 6, 2013

0.6.3

Mar 29, 2013

0.6.2

Mar 20, 2013

0.6.1

Mar 1, 2013

0.6.0

Feb 6, 2013

0.5a pre-release

Jan 2, 2013

0.4a pre-release

Nov 14, 2012

0.2

Sep 7, 2011

0.1

Aug 3, 2011

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