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Bioinformatics Advance Access published online on August 12, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn429
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SeqMap : mapping massive amount of oligonucleotides to the genome

Hui Jiang 1 and Wing Hung Wong 2,*

1 Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, USA.
2 Department of Statistics, Stanford University, Stanford, California 94305, USA.

*To whom correspondence should be addressed. Prof. Wing Hung Wong, E-mail: whwong{at}stanford.edu


  Abstract

Summary: SeqMap is a tool for mapping large amount of short sequences to the genome. It is designed for finding all the places in a reference genome where each sequence may come from. This task is essential to the analysis of data from ultra high throughput sequencing machines. With a carefully designed index-filtering algorithm and an efficient implementation, SeqMap can map tens of millions of short sequences to a genome of several billions of nucleotides. Multiple substitutions and insertions/deletions of the nucleotide bases in the sequences can be tolerated and therefore detected. SeqMap supports FASTA input format and various output formats, and provides command line options for tuning almost every aspect of the mapping process. A typical mapping can be done in a few hours on a desktop PC. Parallel use of SeqMap on a cluster is also very straightforward.

Associate Editor: Dr. Limsoon Wong

Received on July 21, 2008; revised on August 8, 2008; accepted on August 8, 2008

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