A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
NOTE!!!! Please read the notice of discontinuation of this project - 08-16-2024
In recent years, changes in personnel, advances in the field, and competing project commitments have made it increasingly challenging to support and continue the development and maintenance of bcbio. At the same time, Nextflow and the nf-core community have seen substantial growth, now hosting numerous globally-used bioinformatics pipelines. We are enthusiastic to join this larger community and to share our best practices within the Nextflow/nf-core framework. We have already contributed to the RNA-seq and small RNA-seq nf-core pipelines and plan to transition other bcbio analyses and new pipelines to nf-core.
Contents¶
User stories
- Somatic (cancer) variants
- Bulk RNA-seq
- Counting cells and transcripts for inDrops3 data
- PureCN analysis of tumor-only samples
- HLA typing
- Small germline variants
- 3’ DGE
- Structural variant calling
- ATAC-seq
- Methylation
- Variant calling using bulk RNA-seq data
- Detecting gene fusions with bulk RNA-seq data
- fast RNA-seq
- Disambiguation
- smallRNA-seq
Infrastructure
- Installation
- Configuration
- Parallel execution
- Outputs
- Project directory:
- Sample directories:
- Why do I have so many coverage metrics? Which one should I use?
- Interpretation of ontarget_pct vs usable_pct
- Interpretation of mosdepth median coverage vs qualimap median coverage
- Interpretation of bcbio(mosdepth) average target coverage vs qualimap mean coverage
- Why I am getting Ontarget_pct > 100?
- Downstream analysis
- Common Workflow Language (CWL)
- Cloud
- Development
Misc
- Users
- Internals
- Presentations
- Teaching
- Single cell RNA-seq analysis
- Cancer tumor-normal variant calling
- Citations
- Variant calling
- Read alignment
- Interval arithmetics.
- Quality control
- Coverage and callable regions
- SNP and indels in germline (WES, WGS, gene panels)
- Structural and copy number variants in germline (WGS data)
- Somatic small variants
- Somatic copy number variants
- Variant annotation
- bulk RNA-seq
- Fusion calling - RNA-seq
- ATAC-seq
- small RNA-seq