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

GATK RNA-Seq Variant Calling in Nextflow

Assembly and intrahost/low-frequency variant calling for viral samples

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

Variant Calling Pipeline Using GATK4 and Nextflow

gatk4 RNA variant calling pipeline

Please consider using/contributing to https://github.com/nf-core/sarek

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

Please consider using/contributing to https://github.com/nf-core/sarek

Assembly and intrahost / low-frequency variant calling for viral samples

A nextflow variant benchmarking pipeline - premature

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

Flujos de trabajos desarrollados y automatizados en el Inmegen para el procesamiento de datos genómicos y transcriptómicos.

a better freebayes-parallel

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

Nextflow DSL2 pipeline to call variants on long read alignment.

Nextflow pipeline for plasmodium SNP calling

Longread PacBio sequencing processing for WGS and PureTarget

Nextflow pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.

Strelka2 nextflow pipeline