Journal Article

The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

Nathan L. Clement, Quinn Snell, Mark J. Clement, Peter C. Hollenhorst, Jahnvi Purwar, Barbara J. Graves, Bradley R. Cairns and W. Evan Johnson

in Bioinformatics

Volume 26, issue 1, pages 38-45
Published in print January 2010 | ISSN: 1367-4803
Published online October 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp614
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing

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Motivation: The advent of next-generation sequencing technologies has increased the accuracy and quantity of sequence data, opening the door to greater opportunities in genomic research.

Results: In this article, we present GNUMAP (Genomic Next-generation Universal MAPper), a program capable of overcoming two major obstacles in the mapping of reads from next-generation sequencing runs. First, we have created an algorithm that probabilistically maps reads to repeat regions in the genome on a quantitative basis. Second, we have developed a probabilistic Needleman–Wunsch algorithm which utilizes _prb.txt and _int.txt files produced in the Solexa/Illumina pipeline to improve the mapping accuracy for lower quality reads and increase the amount of usable data produced in a given experiment.

Availability: The source code for the software can be downloaded from http://dna.cs.byu.edu/gnumap.

Contact: nathanlclement@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6305 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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