SWAP454 v43803 (Call SNPs in 454 read data)
SWAP454 is a program for calling SNPs using 454 read data. It aligns to the genome using a novel alignment tool called QueryLookupTable, and looks for unique alignments to a reference. Using those alignments, a coverage map file is built that indicates the coverage and base calls for each base position on the reference. This coverage is filtered using a neighborhood-quality score method. The coverage map file can be transformed into individual SNP calls. SWAP454 also includes code for creating improved quality scores for 454 read data that has been incorporated into the algorithm used by 454 Life Sciences.