omnomnomics

omnomnomics is an installable Snakemake application for modular RNA-seq, ATAC-seq, and ChIP-seq processing on Slurm-based HPC systems. It supports complete FASTQ-to-analysis workflows and selective stage ranges for resuming or reusing existing data.

The pipeline provides:

  • FASTQ trimming, FastQC, alignment, lane merging, and assay-aware BAM filtering
  • alignment and experiment-level quality-control reports
  • stranded RNA BigWigs and grouped UCSC track hubs
  • RNA count tables and DESeq2 differential-expression analysis
  • replicate-aware ATAC/ChIP peak calling, peak QC, differential chromatin analysis, motif analysis, and signal summaries
  • auditable run configuration, tool-version, command, scheduler, and stage logs
  • retention policies and a soft project-size guard for quota-constrained HPC work

Start here

  1. Install omnomnomics and configure the HPC site.
  2. Prepare an experiment directory with a FASTQ/ folder.
  3. Read the quickstart and the page for your assay.
  4. Run a dry run before dispatching a full analysis.
omnomnomics rna \
  -i /path/to/experiment \
  -g GRCh38 \
  --dry-run

Remove --dry-run to submit the controller job. The controller runs Snakemake on one Slurm allocation and dispatches worker jobs for individual rules. You do not need to wrap the omnomnomics command in sbatch.

Choose an assay

Assay Command Principal terminal outputs
RNA-seq omnomnomics rna count tables, DE results, stranded BigWigs, track hubs
ATAC-seq omnomnomics atac consensus peaks, peak QC, counts, differential regions
ChIP-seq omnomnomics chip narrow or broad features, QC, counts, differential regions

Use omnomnomics --version to report the installed release and omnomnomics <assay> --help for the authoritative options of that release.