Variant Calling Pipeline Using GATK4 and Nextflow

See the main fork of this repository here >>>

A pipeline for bioinformatics analysis of bacterial genomes

Genotype Imputation Pipeline for H3Africa

DEPRECIATED! Please use nf-core/tools instead

Repository of Nextflow+BioContainers workflows

A bioinformatics best-practice analysis pipeline for the analysis of shallow whole genome sequencing (sWGS) data for the identification of copy number alterations (CNAs).

pathogen agnostic general workflow for genome assembly of Illumina paired-end sequence data

Generate simulated illumina sequence reads from a reference sequence

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

A pipeline for assembling and annotation of vectors

A cgMLST pipeline based on the KMA aligner

Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.

A Nextflow Assembly Pipeline for Downstream Analysis of long reads (ONT) - Genome Assembly .

Reproducible evaluation of short read mappers

Pre-processing of multiplexed CRISPR / shRNA Screens (deprecated)

Mask Pathogens for Outbreak Analysis

A transcript annotation for incomplete or poorly annotated genomes using nanopore reads

This repo contains example code for running NVIDIA Parabricks using NextFlow. The examples here are minimal and are meant as a starting point to show users how to connect Parabricks and NextFlow.

Retrieve Files from VBCF Sequencing Facility