Autoseq: Python command line tool to analyze clinical genomics data

Autoseq can be used to analyze clinical genomics data which is generated by Karolinska Hospital. It has two major piplines called Alascca, LiqBio. Alascca pipeline is used for ALASCCA study which is A randomized, placebo-controlled, multicenter study of the value of low dose aspirin (ASA) added to patients with colorectal cancer. LiqBio pipeline is used to analyze cell free t-DNA from blood samples in PROBIO study, Prostate cancer. Liqbio Pipeline has two versions, one with umi processing steps and another normal pipeline.

Source code GitHub
License Apache License 2.0
Packages Python 2.7
Q&A Questions & Answers

CLI Options

  • Pipelines

    • alascca
    • liqbio
  • Tool

    • autoseq
    • generate_ref