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Description

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.

Code Quality Rank: L3
Programming language: Python
License: MIT License
Latest version: v1.2.8

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README

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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.

Build Status Documentation status DOI

Features

Quick start

  1. Install bcbio-nextgen with all tool dependencies and data files: shell script 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.
  1. Automatically create a processing description of sample FASTQ and BAM files from your project, and a CSV file of sample metadata: shell script 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.
  1. Run analysis, distributed across 8 local cores: shell script 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.


*Note that all licence references and agreements mentioned in the bcbio-nextgen README section above are relevant to that project's source code only.