CBIO open source pipelines for omics data
The Computational Biology division at UCT hosts a range streamlined open-source pipelines built using existing open source tools as well as custom scripts. Although these pipelines are primarily run on the UCT high-performance cluster they are designed with reproducibility and ease of use (Nextflow), version control (GitHub) and portability (Docker and Singularity) in mind.
CBIO pipelines are available for:
- Metagenomics (WGS)
- 16S rRNA amplicon sequencing
- RNAseq (human)
- Array-based genotyping
- Human whole genome and exome sequencing