Generate and run ENCODE analysis pipelines
pipeline-guideskillsetup L3★35
ammawla/encode-toolkit ↗What it does
Execute ENCODE GUIDE processing pipeline
Best for
Selecting and executing appropriate pipeline for your genomics workflow.
Inputs
- · Aligned BAM files
Outputs
- · Peak calls (narrowPeak/broadPeak format)
- · Signal tracks (bigWig)
- · Contact/interaction matrix
- · Plots/visualizations (PNG/PDF/SVG)
Requires
- · Nextflow
- · Docker
- · BWA/Bowtie2 aligner
- · MACS2 peak caller
- · IDR (irreproducible discovery rate)
- · Juicer
- · HiCCUPS
Preconditions
- · Reference genome indexed
- · FASTQ files available
- · Nextflow/Docker installed
Failure modes
- · Poor FASTQ quality (low pass rate)
- · Reference genome mismatch
- · Memory exhaustion on large datasets
- · Adapter contamination
Trust signals
- · ENCODE consortium standards documented
- · Maintained in ammawla/encode-toolkit
- · Peer-reviewed publications cited