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

nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data

Schmid Steven, Julian Timothy R., Tamminen Manu
doi: https://doi.org/10.1101/399782
Schmid Steven
1Department of Biosystems Science and Engineering, ETH Zürich, Zürich, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Julian Timothy R.
2Eawag, Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
3Swiss Tropical and Public Health Institute, Basel, Switzerland
4University of Basel, Basel, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tamminen Manu
5Department of Biology, University of Turku, Turku, Finland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Advancements in DNA sequencing technologies rapidly change the landscape of modern biology. The novel next-generation sequencing (NGS) applications often have special requirements regarding experimental data processing. Software tools developed and used for novel applications are generally designed for specific use cases and as such may be difficult to adapt to new uses. Simultaneously, software tools designed to be general are often difficult to adapt to special use cases.

Here, we present nsearch, a modern open source C++11 library and command-line tool for biological sequence data processing. nsearch offers commonly used components for handling of biological sequences including paired-end read merging, quality filtering and sequence similarity searching. nsearch can either be embedded natively into other C++ applications or be packaged as a standalone executable.

Functionality and performance of nsearch is shown using benchmark data created using the Rfam 13 database. Benchmarking against common general purpose tools USEARCH and VSEARCH demonstrates that nsearch delivers performance comparable these state-of-the-art tools.

nsearch is available on GitHub under the permissive BSD-3-clause license: https://github.com/stevschmid/nsearch

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 4.0 International license.
Back to top
PreviousNext
Posted August 25, 2018.
Download PDF
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.
nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data
(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
nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data
Schmid Steven, Julian Timothy R., Tamminen Manu
bioRxiv 399782; doi: https://doi.org/10.1101/399782
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
nsearch: An open source C++ library for processing and similarity searching of next-generation sequencing data
Schmid Steven, Julian Timothy R., Tamminen Manu
bioRxiv 399782; doi: https://doi.org/10.1101/399782

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 (4087)
  • Biochemistry (8762)
  • Bioengineering (6479)
  • Bioinformatics (23341)
  • Biophysics (11750)
  • Cancer Biology (9149)
  • Cell Biology (13247)
  • Clinical Trials (138)
  • Developmental Biology (7416)
  • Ecology (11369)
  • Epidemiology (2066)
  • Evolutionary Biology (15087)
  • Genetics (10399)
  • Genomics (14009)
  • Immunology (9121)
  • Microbiology (22040)
  • Molecular Biology (8779)
  • Neuroscience (47367)
  • Paleontology (350)
  • Pathology (1420)
  • Pharmacology and Toxicology (2482)
  • Physiology (3704)
  • Plant Biology (8050)
  • Scientific Communication and Education (1431)
  • Synthetic Biology (2208)
  • Systems Biology (6016)
  • Zoology (1249)