Document Detail


PE-Assembler: de novo assembler using short paired-end reads.
MedLine Citation:
PMID:  21149345     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
MOTIVATION: Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized.
RESULT: We present a method that eschews the traditional graph-based approach in favor of a simple 3' extension approach that has potential to be massively parallelized. Our results show that it is able to obtain assemblies that are more contiguous, complete and less error prone compared with existing methods.
AVAILABILITY: The software package can be found at http://www.comp.nus.edu.sg/~bioinfo/peasm/. Alternatively it is available from authors upon request.
CONTACT: ksung@comp.nus.edu.sg; sungk@gis.a-star.edu.sg
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors:
Pramila Nuwantha Ariyaratne; Wing-Kin Sung
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Publication Detail:
Type:  Journal Article     Date:  2010-12-12
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  27     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2011 Jan 
Date Detail:
Created Date:  2011-01-11     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  167-74     Citation Subset:  IM    
Affiliation:
Computational & Mathematical Biology Group, Genome Institute of Singapore, 138672 and School of Computing, National University of Singapore, Singapore 117543.
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