The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing Export

@article{citeulike:6021371, 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 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: nathanlclement@gmail.com 10.1093/bioinformatics/btp614}, author = {Clement, Nathan L. and Snell, Quinn and Clement, Mark J. and Hollenhorst, Peter C. and Purwar, Jahnvi and Graves, Barbara J. and Cairns, Bradley R. and Johnson, W. Evan}, citeulike-article-id = {6021371}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp614}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btp614v1/.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btp614v1/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19861355}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19861355}, day = {27}, doi = {10.1093/bioinformatics/btp614}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {assembly, bioinformatics, genomics, sequencing, software}, month = {October}, pages = {btp614+}, posted-at = {2009-10-31 00:48:49}, priority = {2}, title = {The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing}, url = {http://dx.doi.org/10.1093/bioinformatics/btp614}, year = {2009} }

TY - JOUR ID - citeulike:6021371 L3 - citeulike-article-id:6021371 N2 - 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: nathanlclement@gmail.com 10.1093/bioinformatics/btp614 JF - Bioinformatics SN - 1460-2059 TI - The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing SP - btp614 KW - assembly KW - bioinformatics KW - genomics KW - sequencing KW - software AU - Clement, Nathan AU - Snell, Quinn AU - Clement, Mark AU - Hollenhorst, Peter AU - Purwar, Jahnvi AU - Graves, Barbara AU - Cairns, Bradley AU - Johnson, Evan PY - 2009/10/27/ UR - http://dx.doi.org/10.1093/bioinformatics/btp614 ER -