Development goals

• Quantifiable: assess variant quality
• Scalable: 1500 whole genome samples
• Reproducible: text-configurable, provenance, version tracking
• Community developed: open source, documented and widely deployable

Quantify quality

Reference materials: http://www.genomeinabottle.org/

Parallel scaling

Infrastructure: http://ipython.org/ipython-doc/dev/parallel/index.html

Reproducible configuration

- files: [NA12878-NGv3-LAB1360-A_1.fastq.gz, NA12878-NGv3-LAB1360-A_2.fastq.gz]
  description: NA12878
  analysis: variant2
  genome_build: GRCh37
  algorithm:
    aligner: bwa
    recalibrate: gatk
    realign: gatk
    variantcaller: [gatk, freebayes, gatk-haplotype]
    coverage_interval: exome
    coverage_depth: high
    platform: illumina
    quality_format: Standard
    validate: NA12878-nist-v2_13-NGv3-pass.vcf

Community developed

• Fully automated installation: CloudBioLinux
• Deployable on multiple clusters (LSF, SGE, Torque)
• Integrated with web platforms (Galaxy, STORMSeq)
• Open source and documented

https://github.com/chapmanb/bcbio-nextgen