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BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species

Schiffthaler, Bastian and Bernhardsson, Carolina and Ingvarsson, Pär and Street, Nathaniel R. (2017). BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species. PloS one. 12 :12 , 1-12
[Journal article]

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Official URL: http://dx.doi.org/10.1371/journal.pone.0189256

Abstract

With the rapid advancement of high throughput sequencing, large numbers of genetic markers can be readily and cheaply acquired, but most current software packages for genetic map construction cannot handle such dense input. Modern computer architectures and server farms represent untapped resources that can be used to enable higher marker densities to be processed in tractable time. Here we present a pipeline using a modified version of OneMap that parallelizes over bottleneck functions and achieves substantial speedups for producing a high density linkage map (N = 20,000). Using simulated data we show that the outcome is as accurate as the traditional pipeline. We further demonstrate that there is a direct relationship between the number of markers used and the level of deviation between true and estimated order, which in turn impacts the final size of a genetic map.

Authors/Creators:Schiffthaler, Bastian and Bernhardsson, Carolina and Ingvarsson, Pär and Street, Nathaniel R.
Title:BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species
Series/Journal:PloS one (1932-6203)
Year of publishing :2017
Volume:12
Number:12
Page range:1-12
Number of Pages:12
Publisher:Public Library of Science
ISSN:1932-6203
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Agris subject categories.:X Agricola extesions > X20 Computer and library sciences
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
Keywords:computing, gene sequencing
URN:NBN:urn:nbn:se:slu:epsilon-e-4751
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4751
Additional ID:
Type of IDID
Web of Science (WoS)000418564200037
ID Code:15277
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(NL, NJ) > Department of Plant Biology (from 140101)
Deposited By: SLUpub Connector
Deposited On:16 Feb 2018 12:13
Metadata Last Modified:16 Feb 2018 12:13

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