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

Open Access
Publisher Website
Google Scholar
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. Contact:nathanlclement@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.