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Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

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ahmedelhosseiny/bcbio-nextgen

 
 

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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.

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Features

Quick start

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

    wget https://raw.githubusercontent.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
    python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local \
          --genomes hg38 --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

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

License

The code is freely available under the MIT license.

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