ZOOM! Zillions of oligos mapped

Lin, H., Zhang, Z., Zhang, M. Q., Ma, B., Li, M. (November 2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24 (21). pp. 2431-7.

URL: http://www.ncbi.nlm.nih.gov/pubmed/18684737
DOI: 10.1093/bioinformatics/btn416

Abstract

MOTIVATION: The next generation sequencing technologies are generating billions of short reads daily. Resequencing and personalized medicine need much faster software to map these deep sequencing reads to a reference genome, to identify SNPs or rare transcripts. RESULTS: We present a framework for how full sensitivity mapping can be done in the most efficient way, via spaced seeds. Using the framework, we have developed software called ZOOM, which is able to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity. AVAILABILITY: ZOOM is freely available to non-commercial users at http://www.bioinfor.com/zoom

Item Type: Paper
Uncontrolled Keywords: Algorithms Contig Mapping/*methods Genome, Human Humans Oligonucleotides/*genetics Sequence Alignment Sequence Analysis, DNA *Software Software Validation
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > Mapping and Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: 1 November 2008
Date Deposited: 22 Feb 2013 21:26
Last Modified: 22 Feb 2013 21:26
PMCID: PMC2732274
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27641

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