The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Initial release of nf-core/clipseq, created with the nf-core template.
- Adapter and quality trimming (
Cutadapt) - Pre-mapping to e.g. rRNA and tRNA sequences (
Bowtie 2) - Genome mapping (
STAR) - UMI-based deduplication (
UMI-tools) - Crosslink identification (
BEDTools) - Bedgraph coverage track generation (
BEDTools) - Peak calling (multiple options):
iCountParacluPureCLIPPiranha
- Motif detection (
DREME) - Quality control:
- Sequencing quality control (
FastQC) - Library complexity (
Preseq) - Regional distribution (
RSeQC)
- Sequencing quality control (
- Overall pipeline run and QC summaries and peak calling comparisons (
MultiQC)