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

WtP: Phage identification via nextflow and docker or singularity

Example Nextflow pipelines and programming techniques

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

Metagenomic classification of long-read sequencing data

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

CAMITAX: Taxon labels for microbial genomes