PineSAP--sequence alignment and SNP identification pipeline.
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.


BACKGROUND
All code used for this pipeline is freely available at the Dendrome project website (http://dendrome.ucdavis.edu/adept2/resequencing.html)
Wegrzyn
Jill L
JL
Department of Plant Sciences, University of California, Davis, CA 95616, USA. jlwegrzyn@ucdavis.edu
Lee
Jennifer M
JM
Liechty
John
J
Neale
David B
DB
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software