marchoeppner

clinical-metagenomics

genomeannotator

ikmb_amplicon_processing

metaorganism-research

Production pipelines for the CRC1182

nf-configs

Centrally managed configuration profiles for various pipelines

trinoflow

Workflow to functionally annotate trinity assemblies

configs

Config files used to define parameters specific to compute environments at different Institutions.

eutaxpro

Taxonomic profiling of eukaroyte genomes using amplicon sequencing

exome-seq

gabi

Genomic Analysis of Bacterial Isolates

gmo-check

Pipeline to check GMOs from short read data

metagenomic-profiling

nf-template

A template for a creating a new nextflow pipeline project.

ngs-qc

QC tools for new sequencing runs (FastQC, FastQ Screen, MultiQC Report)

Augustus

Genome annotation with AUGUSTUS

augustus-container

Containerize Augustus ComPred

BloodTypingArray

The software for the Intitutes genotyping array based blood group typing

LaMeta

LaMeta - getting more from your metagenomic data (like you used to...)

ncrna-annotation

Annotate ncRNAs from assemblies using Rfam

nf-mlst

Perform (cg)MLST on a set of bacterial genome assemblies

nf-testdata

Test datasets for nextflow pipeline

ngs-dm

pathoscope2-docker

Instructions for a docker container with pathoscope2

read-qc

NGS read qc

sanger-profile

Profile amplicons from Sanger sequencing with optional assembly

sanger-taxonomy

Taxonomic profiling of Sanger amplicons

SatsumaKraken

Build instructions for Satsuma2+ Kraken Docker container

scripts

Collection of various scripts

test-datasets

Test data to be used for automated testing with the nf-core pipelines

VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)