d4straub

functionalmetagenomics

Assembly-free functional metagenomics pipeline with KneadData and HUMAnN3

ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

bacass

Simple bacterial assembly and annotation pipeline

genomeassembler

mag

Assembly and binning of metagenomes

modules

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

nf-core-configs

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

rnadeseq

Downstream differential gene expression analysis with DESeq2 package

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

nf-core-readsimulator

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

pipesidle

Multipe region amplicon sequencing analysis with SMURF via Sidle in QIIME2

test-datasets

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

vm-playbooks

Ansible playbooks for QIIME 2 environments