Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Repository to host tool-specific module files for the Nextflow DSL2 community!

Pipeline to fetch metadata and raw FastQ files from public databases

Call and score variants from WGS/WES of rare disease patients.

A comprehensive cancer DNA/RNA analysis and reporting pipeline

Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

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 t…

Pipeline to evaluate and validate the accuracy of variant calling methods in genomic research

A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.

Converts bam or cram files to fastq format and does quality control.

A pipeline to identify (and remove) certain sequences from raw genomic data. Default taxon to identify (and remove) is Homo sapiens. Removal is optional.

Analysis pipeline for the functional annotation and translation of somatic SNVs/InDels and copy number abberations for precision cancer medicine using PCGR

Time to learn DSL2

Nextflow pipeline to convert VCF files into MAF files.

Create panel of normals for Mutect2 & CNVKit

Intersects Strelka2 and Mutect2 VCF files

Nextflow pipeline to transform (g)VCF files to matrices for statistical analysis.