Document Detail


Fulcrum: condensing redundant reads from high-throughput sequencing studies.
MedLine Citation:
PMID:  22419786     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: Ultra-high-throughput sequencing produces duplicate and near-duplicate reads, which can consume computational resources in downstream applications. A tool that collapses such reads should reduce storage and assembly complications and costs.
RESULTS: We developed Fulcrum to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory.
Authors:
Matthew S Burriesci; Erik M Lehnert; John R Pringle
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2012-03-13
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  28     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 May 
Date Detail:
Created Date:  2012-05-10     Completed Date:  2012-12-05     Revised Date:  2013-06-26    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1324-7     Citation Subset:  IM    
Affiliation:
Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Gene Expression Profiling
High-Throughput Nucleotide Sequencing / methods*
Humans
Pseudomonas / genetics
Sequence Analysis, DNA / methods
Software*
Grant Support
ID/Acronym/Agency:
5 T32 HG000044/HG/NHGRI NIH HHS
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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