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


BACKGROUND
The source code for the software can be downloaded from http://dna.cs.byu.edu/gnumap.
Department of Computer Science, Department of Statistics, Brigham Young University, Provo, UT 84602, USA. nathanlclement@gmail.com
Nathan L
NL
Clement
Quinn
Q
Snell
Mark J
MJ
Clement
Peter C
PC
Hollenhorst
Jahnvi
J
Purwar
Barbara J
BJ
Graves
Bradley R
BR
Cairns
W Evan
WE
Johnson
D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004247:DNA / Q000235:genetics*; D003627:Data Interpretation, Statistical; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004247:DNA