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ILIAD: Suite of Genomic Data Workflows

Iliad is a multi-functional toolkit comprised of genomic data processing pipelines implemented via the Snakemake workflow management system, Singularity or Docker container, and a handful of Conda environments. Instances of any Singularity or Docker containers and Conda environments are automatically pulled down and created to build the right execution environment during workflow runtime, making light of the numerous required bioinformatic third-party software tools and dependencies. The multi-functional feature is supported by a modularized Snakemake workflow design and includes independent Snakemake workflows to accommodate many forms of genomic data and translate them to comprehensible genotypes in a variant call format (VCF) file.

https://youtu.be/9CCnaLlUFG4

Quick intro about Iliad

These are the currently supported genomic data starting points below:

  • Raw Sequence Read Data (.fq)
  • Stored Sequence Read Data (.cram)
  • SNP Array Data (.idat)
  • VCF data (.vcf/.vcf.gz)

Iliad is set apart by empowering genetic data management and processing for reference and target datasets independently or simultaneously.

What you need to do:

  • Follow the Installation and How-To Guides for the appropriate module or submodule you are interested in running
  • Add your working directory PATH to the top of the configuration file Iliad/config/config.yaml
  • provide an FTP link for the desired open-source raw or stored data into an Excel file found in the cloned Iliad/config directory OR migrate locally hosted data into the cloned Iliad repository

What Iliad will do:

  • Deliver the GWAS data you need for your analyses as optimized VCF output

Getting started

  • Please read our paper for a full understanding of how Iliad can best serve you and your genetic data processing road blocks replace with paper link here.
  • Quickly learn how to install Iliad - visit the Installation page
  • Start processing your data right away by following one of the HOW-TO GUIDES on Iliad modules or Submodules

    • Modules

      • Raw Sequence Read Data (.fq)
      • Stored Sequence Read Data (.cram)
      • SNP Array Data (.idat)

Iliad Workflow Schematics

Main Modules

image

A comprehensive Submodule ****************************

image

getting_started/installation getting_started/GCP getting_started/academic getting_started/docker getting_started/demo getting_started/config

tutorial/raw_sequence tutorial/stored_sequence tutorial/snp_array

tutorial/lift_and_merge tutorial/liftover tutorial/merge_ref_target

projectinfo/citing projectinfo/more_resources projectinfo/comingsoon projectinfo/container_images projectinfo/faq projectinfo/contributing projectinfo/credits projectinfo/changelog projectinfo/license