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

minimal example implementations for bioinformatics workflow managers

VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

Long read QC, assembly and scaffolding pipeline

customizable pipeline to identify viral sequences from (meta)genomic data

Alignment-based Scrubbing pipeline

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework

A flexible pipeline for complete analysis of bacterial genomes

Snakemake pipelines for nanopore sequencing data archiving and processing

VAPiD: Viral Annotation and Identification Pipeline

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

Snakemake pipeline to automate a standard PSASS workflow

Pipelines for the production of Treeval data