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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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
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.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.shell script
cd project1/work
bcbio_nextgen.py ../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.
*Note that all licence references and agreements mentioned in the bcbio-nextgen README section above
are relevant to that project's source code only.
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