RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

A flexible pipeline for complete analysis of bacterial genomes

A curated collection of Nextflow implementation patterns

Assembly and binning of metagenomes

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Example Nextflow pipelines and programming techniques

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

WtP: Phage identification via nextflow and docker or singularity

Renders a collection of sequences into a pangenome graph. https://doi.org/10.1093/bioinformatics/btae609.

Surveillance of pathogens using population genomics and sequencing

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

CAMITAX: Taxon labels for microbial genomes