All Published Workflows
8 workflows that have been reviewed and published
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
Workflow figure created on BioRender.com. Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut ...
Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
A snakemake-wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, a...
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
This repo builds on code by Mick Watson who wrote a blog post and follow up about a quick way to test the viabili...
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
nf-core/bactmap is a bioinformatics best-practice analysis pipeline for mapping short reads from bacterial WGS to a refere...
Simple bacterial assembly and annotation pipeline
nf-core/bacass is a bioinformatics best-practice analysis pipeline for simple bacterial assembly and annotation. The pipel...