This repository contains a collection of genomic pipelines developed by the UCSC Computational Genomics Lab.
To install these pipelines, just type: pip install toil-scripts
Entrypoints are supplied to pipelines that work with the current stable release of Toil:
- Fastq to BAM alignment:
toil-bwa - CGL RNA-seq Pipeline (hg38):
toil-rnaseq - UNC best practices RNA-seq pipeline (hg19):
toil-rnaseq-unc - SplAdder alternative splicing pipeline:
toil-spladder - GATK exome variant pipeline:
toil-exome
Each pipeline has its own README that provides 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.