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bcbio-dnanexus-wrapper

Repository to hold wrapper apps for bcbio CWL on DNAnexus

bcbio-nextgen

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

bcbio-nextgen-vm

Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines

bcbio-utils

Helper scripts for bcbio-nextgen

bcbio-validation-checker

Compare validation outputs from bcbio against existing truth sets

bcbio.github.io

Blue Collar Bioinformatics website

bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants

bcbio_docker

Automated Docker builds for bcbio

bcbio_rnaseq_output_example

example of bcbio RNAseq output to test bcbioRnaseq R package

bcbio_srnaseq_output_example

Example of small RNAseq analysis with bcbio

bcbio_validation_workflows

A community menagarie of automated variant validations using bcbio and the Common Workflow Language

bcbio_validations

Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses

bcbior

R package with well defined templates for most common pipelines

bcbior-test-data

repository to host small dataset for bcbioR package

bioconda-recipes

Conda recipes for the bioconda channel.

cloudbiolinux

CloudBioLinux: configure virtual (or real) machines with tools for biological analyses

hivdrm

Detect HIV Drug Resitant Mutations using amplicon sequencing data

icr142-validation

Preparation scripts and bcbio integration for the ICR142 NGS validation series

scramble

test_bcbio_cwl

Test workflows, run scripts and data for bcbio Common Workflow Language integration