Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

s-aligner: a greedy algorithm for non-greedy de novo genome assembly

View ORCID ProfileJuanjo Bermúdez
doi: https://doi.org/10.1101/2021.02.02.429443
Juanjo Bermúdez
1Contignant Technologies SL c/Emigrant 30, Barcelona, Spain (08906)
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Juanjo Bermúdez
  • For correspondence: juanjo75es@gmail.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Genome assembly is a fundamental tool for biological research. Particularly, in microbiology, where budgets per sample are often scarce, it can make the difference between an inconclusive result and a fully valid conclusion. Identifying new strains or estimating the relative abundance of quasi-species in a sample are some example tasks that can’t be properly accomplished without previously generating assemblies with little structure ambiguity and covering most of the genome. In this work, we present a new genome assembly tool based on a greedy strategy. We compare the results obtained applying this tool to the results obtained with previously existing software. We find that, when applied to viral studies, comparatively, the software we developed often gets far larger contigs and higher genome fraction coverage than previous software. We also find a significant advantage when applied to exceptionally large virus genomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://contignant.com

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted February 02, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
s-aligner: a greedy algorithm for non-greedy de novo genome assembly
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
s-aligner: a greedy algorithm for non-greedy de novo genome assembly
Juanjo Bermúdez
bioRxiv 2021.02.02.429443; doi: https://doi.org/10.1101/2021.02.02.429443
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
s-aligner: a greedy algorithm for non-greedy de novo genome assembly
Juanjo Bermúdez
bioRxiv 2021.02.02.429443; doi: https://doi.org/10.1101/2021.02.02.429443

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3479)
  • Biochemistry (7318)
  • Bioengineering (5296)
  • Bioinformatics (20196)
  • Biophysics (9976)
  • Cancer Biology (7703)
  • Cell Biology (11250)
  • Clinical Trials (138)
  • Developmental Biology (6417)
  • Ecology (9916)
  • Epidemiology (2065)
  • Evolutionary Biology (13278)
  • Genetics (9352)
  • Genomics (12552)
  • Immunology (7674)
  • Microbiology (18939)
  • Molecular Biology (7417)
  • Neuroscience (40889)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2126)
  • Physiology (3140)
  • Plant Biology (6838)
  • Scientific Communication and Education (1270)
  • Synthetic Biology (1891)
  • Systems Biology (5296)
  • Zoology (1085)