Iliad is a suite of Snakemake workflows for genomic data processing. The modularization feature of Snakemake accomodates raw sequence data (.fq), stored sequence data (.cram), Illumina microarray data (.idat), and variant call format data (.vcf).
Please visit our documentation hosted on Read The Docs: https://iliad.readthedocs.io/
If you use this workflow in your publication, please cite the corresponding article:
Herrick, N., Walsh, S. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics 24, 424 (2023). https://doi.org/10.1186/s12859-023-05548-x
ILIAD
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.
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/configdirectory 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
- Please read our paper for a full understanding of how Iliad can best serve you and your genetic data processing road blocks:
Herrick, N., Walsh, S. ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. BMC Bioinformatics 24, 424 (2023). https://doi.org/10.1186/s12859-023-05548-x
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Quickly learn how to install Iliad - visit the Installation page at https://iliad.readthedocs.io/
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Start processing your data right away by following one of the
HOW-TO GUIDESon Iliad modules or Submodules