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Repository to host tool-specific module files for the Nextflow DSL2 community!
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Assembly and intrahost/low-frequency variant calling for viral samples
Config files used to define parameters specific to compute environments at different Institutions
Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.
Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads
A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies
A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies
A pipeline for bioinformatics analysis of bacterial genomes
A nf-core pipeline for untargeted whole genome reconstruction with iSNV detection from metagenomic samples.
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
Nextflow Alignment Pipeline - from fastq.gz to sorted bam/cram with ease
A simple nextflow pipeline for running kraken2 and bracken in a docker container
A pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis with a focus on clinical decision making as well as research
Pipeline for identifying, annotation, and quantifying phage sequences in (meta)-genomic sequences.
Finding regions of similarity between plasmids
A simple pipeline for bacterial assembly and quality control
Nextflow DSL2 pipeline to align short and long reads to genome assembly. This workflow is part of the Tree of Life production suite.
A tooL for Prokaryotic Phylogeny And Clustering Analysis