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The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing.
Bioinformatics. 2009 Oct 27;
Authors: Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE
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 paper, we present GNUMAP (Genomic Nextgeneration 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: [email protected].
PMID: 19861355 [PubMed - as supplied by publisher]
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The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing.
Bioinformatics. 2009 Oct 27;
Authors: Clement NL, Snell Q, Clement MJ, Hollenhorst PC, Purwar J, Graves BJ, Cairns BR, Johnson WE
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 paper, we present GNUMAP (Genomic Nextgeneration 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: [email protected].
PMID: 19861355 [PubMed - as supplied by publisher]
More...