• search hit 1 of 2
Back to Result List

Improving draft genome contiguity with reference-derived in silico mate-pair libraries

  • Background Contiguous genome assemblies are a highly valued biological resource because of the higher number of completely annotated genes and genomic elements that are usable compared to fragmented draft genomes. Nonetheless, contiguity is difficult to obtain if only low coverage data and/or only distantly related reference genome assemblies are available. Findings In order to improve genome contiguity, we have developed Cross-Species Scaffolding—a new pipeline that imports long-range distance information directly into the de novo assembly process by constructing mate-pair libraries in silico. Conclusions We show how genome assembly metrics and gene prediction dramatically improve with our pipeline by assembling two primate genomes solely based on ∼30x coverage of shotgun sequencing data.

Export metadata

Additional Services

Search Google Scholar Statistics
Metadaten
Author details:José Horacio Grau, Thomas Hackl, Klaus-Peter Koepfli, Michael HofreiterORCiDGND
DOI:https://doi.org/10.1093/gigascience/giy029
ISSN:2047-217X
Title of parent work (English):GigaScience
Publisher:Oxford University Press
Place of publishing:Oxford
Publication type:Article
Language:English
Date of first publication:2018/04/21
Publication year:2018
Release date:2018/11/09
Tag:genome assembly; in silico; mate-pairs; scaffolding; shotgun sequencing
Volume:7
Issue:5
First page:1
Last Page:6
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
DDC classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Peer review:Referiert
Publishing method:Open Access
License (German):License LogoCC-BY - Namensnennung 4.0 International
External remark:Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 477
Accept ✔
This website uses technically necessary session cookies. By continuing to use the website, you agree to this. You can find our privacy policy here.