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. Preprints2022, 2022080191. https://doi.org/10.20944/preprints202208.0191.v1
Menzel, P. Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation. Preprints 2022, 2022080191. https://doi.org/10.20944/preprints202208.0191.v1
Menzel, P. Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation. Preprints2022, 2022080191. https://doi.org/10.20944/preprints202208.0191.v1
APA Style
Menzel, P. (2022). Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation. Preprints. https://doi.org/10.20944/preprints202208.0191.v1
Chicago/Turabian Style
Menzel, P. 2022 "Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation" Preprints. https://doi.org/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.
bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
