Bioinformatics. 2010 Jan 1;26(1):38-45. Epub 2009 Oct 27.

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

Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE.

Source

Department of Computer Science, Department of Statistics, Brigham Young University, Provo, UT 84602, USA. nathanlclement@gmail.com

Abstract

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.

PMID:: 19861355; [PubMed - indexed for MEDLINE]

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