This repository contains a nextflow workflow that can be used to de novo assemble plasmid sequences from Oxford Nanopore data.

This repository contains a nextflow workflow that can be used to de novo assemble plasmid sequences from Oxford Nanopore data to allow users to verify complete artificial contructs.

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker or singularity is installed.

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.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-clone-validation --help

to see the options for the workflow.

Workflow outputs

The primary outputs of the workflow include:

• a consensus fasta file for each sample
• a csv showing the pass or fail status of each sample
• a feature table containing annotations for each of the samples
• an HTML report document detailing the primary findings of the workflow.

Download the required database

The workflow requires a database which can be downloaded and unzipped using these commands.

wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-clone-validation/wf-clone-validation-db.tar.gz
tar -xzvf wf-clone-validation-db.tar.gz

The location of the database will need to be specified with the --db_directory parameter.

• nextflow
• docker