Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation

Version 1 : Received: 7 August 2022 / Approved: 10 August 2022 / Online: 10 August 2022 (04:37:01 CEST)

How to cite: Menzel, P. Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation. Preprints 2022, 2022080191 (doi: 10.20944/preprints202208.0191.v1). Menzel, P. Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation. Preprints 2022, 2022080191 (doi: 10.20944/preprints202208.0191.v1).

Abstract

With the advancement of long-read sequencing technologies and their more widespread use for bacterial genomics, several methods for generating genome assemblies from error-prone long reads have been developed. These are complemented by various tools for assembly polishing using either long reads, short reads, or reference genomes. End users are therefore left with a plethora of possible combinations of programs for obtaining a final trusted assembly. Hence, there is also the need for measuring completeness and accuracy of such assemblies, for which, again, several evaluation methods implemented in various programs are available. In order to automatically run all these programs, I developed two workflows for the workflow management system Snakemake for bacterial genome assembly and evaluation of assemblies, which provide end users with an easy-to-run method for both tasks. The workflows are available as open source software under the MIT license at https://github.com/pmenzel/ont-assembly-snake and https://github.com/pmenzel/score-assemblies.

Supplementary and Associated Material

https://github.com/pmenzel/ont-assembly-snake: ont-assembly-snake Snakemake workflow
https://github.com/pmenzel/score-assemblies: score-assemblies Snakemake workflow

Keywords

bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake

Subject

LIFE SCIENCES, Molecular Biology

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