PineSAP—sequence alignment and SNP identification pipeline

Summary: 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. Availability: All code used for this pipeline is freely available at the Dendrome project website (http://dendrome.ucdavis.edu/adept2/resequencing.html) Contact: jlwegrzyn@ucdavis.edu