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Bioinformatics. 2010 Jan 1;26(1):38-45. doi: 10.1093/bioinformatics/btp614. Epub 2009 Oct 27.

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

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  • 1Department of Computer Science, Department of Statistics, Brigham Young University, Provo, UT 84602, USA.



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.


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.


The source code for the software can be downloaded from

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