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

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

Bernardo J. Clavijo, Gonzalo Garcia Accinelli, Jonathan Wright, Darren Heavens, Katie Barr, Luis Yanes, Federica Di-Palma
doi: https://doi.org/10.1101/110999
Bernardo J. Clavijo
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gonzalo Garcia Accinelli
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan Wright
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Darren Heavens
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katie Barr
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luis Yanes
Earlham Institute, Norwich Research Park, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Federica Di-Palma
Earlham Institute, Norwich Research Park, UK
  • 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

Producing high-quality whole-genome shotgun de novo assemblies from plant and animal species with large and complex genomes using low-cost short read sequencing technologies remains a challenge. But when the right sequencing data, with appropriate quality control, is assembled using approaches focused on robustness of the process rather than maximization of a single metric such as the usual contiguity estimators, good quality assemblies with informative value for comparative analyses can be produced. Here we present a complete method described from data generation and qc all the way up to scaffold of complex genomes using Illumina short reads and its application to data from plants and human datasets. We show how to use the w2rap pipeline following a metric-guided approach to produce cost-effective assemblies. The assemblies are highly accurate, provide good coverage of the genome and show good short range contiguity. Our pipeline has already enabled the rapid, cost-effective generation of de novo genome assemblies from large, polyploid crop species with a focus on comparative genomics.

Availability w2rap is available under MIT license, with some subcomponents under GPL-licenses. A ready-to-run docker with all software pre-requisites and example data is also available.

http://github.com/bioinfologics/w2rap

http://github.com/bioinfologics/w2rap-contigger

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 February 22, 2017.
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.
W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read 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.
Share
W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data
Bernardo J. Clavijo, Gonzalo Garcia Accinelli, Jonathan Wright, Darren Heavens, Katie Barr, Luis Yanes, Federica Di-Palma
bioRxiv 110999; doi: https://doi.org/10.1101/110999
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data
Bernardo J. Clavijo, Gonzalo Garcia Accinelli, Jonathan Wright, Darren Heavens, Katie Barr, Luis Yanes, Federica Di-Palma
bioRxiv 110999; doi: https://doi.org/10.1101/110999

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 (1540)
  • Biochemistry (2499)
  • Bioengineering (1756)
  • Bioinformatics (9720)
  • Biophysics (3927)
  • Cancer Biology (2990)
  • Cell Biology (4230)
  • Clinical Trials (135)
  • Developmental Biology (2651)
  • Ecology (4124)
  • Epidemiology (2033)
  • Evolutionary Biology (6930)
  • Genetics (5239)
  • Genomics (6531)
  • Immunology (2205)
  • Microbiology (7004)
  • Molecular Biology (2780)
  • Neuroscience (17399)
  • Paleontology (127)
  • Pathology (432)
  • Pharmacology and Toxicology (712)
  • Physiology (1067)
  • Plant Biology (2514)
  • Scientific Communication and Education (646)
  • Synthetic Biology (835)
  • Systems Biology (2698)
  • Zoology (438)