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

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

GATK RNA-Seq Variant Calling in Nextflow

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.

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

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

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

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

Longread PacBio sequencing processing for WGS and PureTarget

Nextflow DSL2 pipeline to call variants on long read alignment.

Flujos de trabajos desarrollados y automatizados en el Intituto Nacional de Medicina Genómica 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 pipeline for whole-genome sequencing (WGS) analysis and variant calling in bacterial genomes using Illumina data, supporting de novo assembly and reference-based analysis.

Nextflow pipeline for plasmodium SNP calling

A containerized bioinformatics pipeline built with Nextflow to identify somatic (acquired) mutations in the tumor of patient-derived xenograft (PDX) models (currently tumor-only mode)