19861355
This reference describes Gnumap.
| PMID | PMID 19861355 |
|---|---|
| Title | The GNUMAP Algorithm: Unbiased Probabilistic Mapping of Oligonucleotides from Next-Generation Sequencing |
| Year | 2009 |
| Journal | Bioinformatics |
| Author | Clement, N. L., Snell, Q., Clement, M. J., Hollenhorst, P. C., Purwar, J., Graves BJ, Cairns BR, Johnson WE |
| Volume | |
| Start page |
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Full text description
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.
