| 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 |
Related Documents
:
|
20084536 - Detection of anaplasma phagocytophilum in amblyomma flavomaculatum ticks (acari: ixodid... 21602336 - Complete genome sequence of the haloalkaliphilic, hydrogen-producing bacterium halanaer... 21632566 - Co-existence of multiple strains of two novel porcine bocaviruses in the same pig, a pr... 21820066 - Mitogenome rearrangement in the cold-water scleractinian coral lophelia pertusa (cnidar... 3015026 - Cloning and expression of the beta-d-galactosidase gene from streptococcus thermophilus... 21489296 - Discovery of permuted and recently split transfer rnas in archaea. |
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: 2013-05-15 |
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. |
Export Citation:
|
APA/MLA Format Download EndNote Download BibTex |
| 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 |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
Previous Document: SAMSCOPE: an OpenGL-based real-time interactive scale-free SAM viewer.
Next Document: TachoSil(R) for postinfarction ventricular free wall rupture.