Lin, H., Zhang, Z., Zhang, M. Q., Ma, B., Li, M. (November 2008) ZOOM! Zillions of oligos mapped. Bioinformatics, 24 (21). pp. 2431-7.
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: | https://repository.cshl.edu/id/eprint/27641 |
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