Bacterial genomes Workflow
This repository contains a nextflow workflow for analysing bacterial genomes. # Introduction
If no reference is included assembly will be completed using flye and polished with medaka. If a reference is provided alignment will be done with mini_align and variant called using medaka. The workflow can optionally run prokka to annotate the resulting consensus sequence.
The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.
It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.
To obtain the workflow, having installed
nextflow, users can run:
nextflow run epi2me-labs/wf-bacterial-genomes --help
to see the options for the workflow.
The primary outputs of the workflow include:
- a FASTA consensus sequence scaffolded from a provided reference sequence,
- a VCF file containing variants in the sample compared to the reference (if provided),
- an HTML report document detailing QC metrics and the primary findings of the workflow,
- (optionally) an annotation of the consensus sequence using prokka.