Blue Collar Bioinformatics

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_validations

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

bcbio.variation.recall

Parallel merging, squaring off and ensemble calling for genomic variants

bcbio_validation_workflows

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

bcbio.github.io

Blue Collar Bioinformatics website

bcbio_docker

Automated Docker builds for bcbio

test_bcbio_cwl

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

icr142-validation

Preparation scripts and bcbio integration for the ICR142 NGS validation series

bcbio-dnanexus-wrapper

Repository to hold wrapper apps for bcbio CWL on DNAnexus

bcbio-utils

Helper scripts for bcbio-nextgen

bcbio_rnaseq_output_example

example of bcbio RNAseq output to test bcbioRnaseq R package

bcbioR

R package with well defined templates for most common pipelines

hivdrm

Detect HIV Drug Resitant Mutations using amplicon sequencing data

cloudbiolinux

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

bcbio-validation-checker

Compare validation outputs from bcbio against existing truth sets

bcbio_srnaseq_output_example

Example of small RNAseq analysis with bcbio

bcbioR-test-data

repository to host small dataset for bcbioR package

bioconda-recipes

Conda recipes for the bioconda channel.

scramble