GATK RNA-Seq Variant Calling in Nextflow

A comprehensive cancer DNA/RNA analysis and reporting pipeline

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

A pipeline for the analysis of CRISPR edited data. It allows the evaluation of the quality of gene editing experiments using targeted next generation sequencing (NGS) data (`targeted`) as well as the discovery of important genes from knock-out or activation CRISPR-Cas9 screens using CRISPR pooled DNA (`screening`).

An automated RNA-seq pipeline using Nextflow

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Whole Exome/Whole Genome Sequencing alignment pipeline

UPHL's Reference Free Pipeline

A pipeline to investigate horizontal gene transfer from NGS data

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.

A Nextflow pipeline for NGS variant calling on SARS-CoV-2. From FASTQ files to normalized and annotated VCF files from GATK, BCFtools, LoFreq and iVar.

An automated ChIP-seq pipeline using Nextfow

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Nextflow pipeline for BWA, BWA2 and STAR alignments

Germline structural variant calling pipeline for short read WGS datasets

A tool suite for a simple, streamlined and rapid evaluation of variant callsets

DupFinder: A tools to detect the duplicated genes using Illumina and Nanopore sequencing data

Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.