This workflow provides an easy way to align Oxford Nanopore reads and gather mapping stats either locally for small amounts of data or at scale in a distributed environment such as a cluster.

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-alignment --help

to see the options for the workflow.

Workflow outputs

The primary outputs of the workflow include:

• A sorted, indexed BAM file containing alignments.
• A CSV containing various mapping stats.
• An HTML report with visualisations of the mapping stats.

• nextflow
• docker
• singularity
• minimap2