This repository contains a collection of genomic pipelines developed by the UCSC Computational Genomics Lab. These pipelines are used on a regular basis in-house and are freely available to anyone who would like to use them.
Pipelines currently supported for the latest version of Toil:
- Fastq to BAM alignment (GATK compatible format)
- Exome variant pipeline
- UNC best practices RNA-seq pipeline
- Our own best practices RNA-seq pipeline (STAR + RSEM, Kallisto)
- Germline variant pipeline
Each pipeline has its own README that provides explicit instructions on how to get up and running. The general dependencies for these pipelines are:
Our group utilizes genomics tools encapsulated within Docker containers for portability. Each of these pipelines can be run locally on your laptop, on a baremetal cluster, or on a cloud provider.
If there are any questions please contact John Vivian (jtvivian@gmail.com). If you find any errors or corrections please feel free to make a pull request. Feedback of any kind is appreciated.