Publication detail

ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing

JUGAS, R. VÍTKOVÁ, H.

Original Title

ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing

Type

journal article in Web of Science

Language

English

Original Abstract

BackgroundStructural variations play an important role in bacterial genomes. They can mediate genome adaptation quickly in response to the external environment and thus can also play a role in antibiotic resistance. The detection of structural variations in bacteria is challenging, and the recognition of even small rearrangements can be important. Even though most detection tools are aimed at and benchmarked on eukaryotic genomes, they can also be used on prokaryotic genomes. The key features of detection are the ability to detect small rearrangements and support haploid genomes. Because of the limiting performance of a single detection tool, combining the detection abilities of multiple tools can lead to more robust results. There are already available workflows for structural variation detection for long-reads technologies and for the detection of single-nucleotide variation and indels, both aimed at bacteria. Yet we are unaware of structural variations detection workflows for the short-reads sequencing platform. Motivated by this gap we created our workflow. Further, we were interested in increasing the detection performance and providing more robust results.ResultsWe developed an open-source bioinformatics pipeline, ProcaryaSV, for the detection of structural variations in bacterial isolates from paired-end short sequencing reads. Multiple tools, starting with quality control and trimming of sequencing data, alignment to the reference genome, and multiple structural variation detection tools, are integrated. All the partial results are then processed and merged with an in-house merging algorithm. Compared with a single detection approach, ProcaryaSV has improved detection performance and is a reproducible easy-to-use tool.ConclusionsThe ProcaryaSV pipeline provides an integrative approach to structural variation detection from paired-end next-generation sequencing of bacterial samples. It can be easily installed and used on Linux machines. It is publicly available on GitHub at https://github.com/robinjugas/ProcaryaSV.

Keywords

Copy number variation; Structural variation; CNV; SV; Bacteria; Pipeline

Authors

JUGAS, R.; VÍTKOVÁ, H.

Released

9. 7. 2024

Publisher

BioMed Central

Location

LONDON

ISBN

1471-2105

Periodical

BMC BIOINFORMATICS

Year of study

25

Number

1

State

United Kingdom of Great Britain and Northern Ireland

Pages from

1

Pages to

13

Pages count

13

URL

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05843-1

Full text in the Digital Library

http://hdl.handle.net/11012/249380

BibTex

@article{BUT189164,
  author="Robin {Jugas} and Helena {Vítková}",
  title="ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing",
  journal="BMC BIOINFORMATICS",
  year="2024",
  volume="25",
  number="1",
  pages="1--13",
  doi="10.1186/s12859-024-05843-1",
  issn="1471-2105",
  url="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-024-05843-1"
}