https://github.com/hammerlab/epidisco

Personalized cancer epitope discovery and peptide vaccine prediction pipeline
https://github.com/hammerlab/epidisco

biokepi epitope-discovery ocaml pipeline

Last synced: 3 months ago
JSON representation

Personalized cancer epitope discovery and peptide vaccine prediction pipeline

• Host: GitHub
• URL: https://github.com/hammerlab/epidisco
• Owner: hammerlab
• License: apache-2.0
• Created: 2016-08-08T19:59:58.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2017-11-14T13:49:29.000Z (about 7 years ago)
• Last Synced: 2023-10-26T06:05:50.903Z (over 1 year ago)
• Topics: biokepi, epitope-discovery, ocaml, pipeline
• Language: OCaml
• Homepage:
• Size: 405 KB
• Stars: 30
• Watchers: 15
• Forks: 6
• Open Issues: 52
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Epidisco

Epidisco is a highly-configurable genomic pipeline. It supports alignment, the

GATK, variant calling, epitope discovery, and vaccine generation.

It uses [Biokepi](https://github.com/hammerlab/biokepi) to construct

[Ketrew](https://github.com/hammerlab/ketrew) workflows which can be scheduled

on many kinds of clusters.

![Pipeline Overview](docs/pipeline.png)

## Usage

Documentation on Biokepi workflows is centralized in the project

[`hammerlab/wobidisco`](https://github.com/hammerlab/wobidisco); a good starting

point is the “Running Local”

[tutorial](https://github.com/hammerlab/wobidisco/blob/master/doc/running-local.md).

## Note on Multiple Samples

You can pass multiple samples into Epidisco, but they will be merged into one

sample (tumor, normal, or tumor RNA) after the alignment & mark duplicates

step. This option to process multiple samples should only be used to e.g. pass

data from biological replicates (or samples you wish to treat as such) into the

pipeline, which fundamentally operates on a tumor, normal, and tumor RNA sample

set.