Journal Article

SeqMap: mapping massive amount of oligonucleotides to the genome

Hui Jiang and Wing Hung Wong

in Bioinformatics

Volume 24, issue 20, pages 2395-2396
Published in print October 2008 | ISSN: 1367-4803
Published online August 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn429
SeqMap: mapping massive amount of oligonucleotides to the genome

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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.

Contact: whwong@stanford.edu

Journal Article.  1628 words. 

Subjects: Bioinformatics and Computational Biology

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