Journal
BIOINFORMATICS
Volume 25, Issue 19, Pages 2609-2610Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btp477
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Funding
- Association Genetics of Natural Genetic Variation and Complex Traits in Pine
- NSF [0501763]
- Division Of Integrative Organismal Systems
- Direct For Biological Sciences [0501763] Funding Source: National Science Foundation
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The Pine Alignment and SNP Identification Pipeline (PineSAP) provides a high-throughput solution to single nucleotide polymorphism (SNP) prediction using multiple sequence alignments from re-sequencing data. This pipeline integrates a hybrid of customized scripting, existing utilities and machine learning in order to increase the speed and accuracy of SNP calls. The implementation of this pipeline results in significantly improved multiple sequence alignments and SNP identifications when compared with existing solutions. The use of machine learning in the SNP identifications extends the pipeline's application to any eukaryotic species where full genome sequence information is unavailable.
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