ATAC-seq peak-calling and QC analysis pipeline

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

Analysis of Chromosome Conformation Capture data (Hi-C)

A Nextflow workflow to generate lift over files for any pair of genomes

A set of workflows written in Nextflow for Genome Annotation.

A pipeline to investigate horizontal gene transfer from NGS data

ExOrthist: a pipeline to extract exon orthologies at any evolutionary distance.

Easy & parallel download of FASTQ files from public repositories (SRA, EGA, GDC)

Draft workflow for pairwise genome comparison. We recommend you use the new nf-core version instead: https://nf-cor.e/pairgenomealign

This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

A set of workflows written in Nextflow for Genome Annotation.

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.