Skip to content
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Branch: master
Clone or download
chapmanb callable: improved error messages with no callable regions
Describe additional issue with bad input reads causing a lack of callable
Latest commit 6ba7300 Mar 24, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
artwork add logo to README and docs Jun 4, 2015
bcbio callable: improved error messages with no callable regions Mar 24, 2019
docs Docs: recommend python3 for bcbio-nextgen-vm installs Mar 18, 2019
tests Switch to yaml.safe_load to avoid warnings from PyYAML 5.1 Mar 23, 2019
.gitignore barcodes_samples now accept files like: Feb 14, 2019
Dockerfile Docs: point to bcbio organization repository Mar 9, 2018 Fix race condition when making pizzly cache. Mar 6, 2019
LICENSE.txt Add MIT license to top level directory. Thanks to @lbeltrame. #54 Jul 18, 2013 Add support for 10x version 2. Oct 30, 2018
README.rst Docs: point to bcbio organization repository Mar 9, 2018
requirements.txt v1.1.2 release Dec 12, 2018 tumor-only germline prioritization: filter based on INFO/EPR Jan 31, 2019


bcbio banner

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.


  • 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

  1. Install bcbio-nextgen with all tool dependencies and data files:

    python /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: -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 ../config/project1.yaml -n 8


See the full documentation and longer analysis-based articles. We welcome enhancements or problem reports using GitHub and discussion on the biovalidation mailing list.



The code is freely available under the MIT license.

You can’t perform that action at this time.