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Welcome to the Computational Research and Development Wiki at The Broad Institute!


ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive.


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.


VAAL is a variant ascertainment algorithm that can be used to detect SNPs, indels, and more complex genetic variants. On bacterial data sets, it achievies very high sensitivity, and near perfect specificity. VAAL can be used to compare reads from one strain to a reference sequence from another strain. It can also be used to compare reads from two strains to each other, using a third strain to determine homology. For example, we have used VAAL to find a single mutation responsible for bacterial resistance: the output of the program was that single mutation and no others. VAAL uses an assisted assembly algorithm that borrows from ALLPATHS.

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