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
[Research article]
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Available under License Creative Commons Attribution. 1MB |
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. | ||||
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Title: | BatchMap: A parallel implementation of the OneMap R package for fast computation of F-1 linkage maps in outcrossing species | ||||
Series Name/Journal: | PloS one | ||||
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: | Research 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: |
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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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