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URL: http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/vaal-manual
Proper Citation: VAAL (RRID:SCR_001184)
Description: A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only.
Abbreviations: VAAL
Resource Type: software resource
Defining Citation: PMID:19079253
Keywords: dna sequence, polymorphism, parallel sequencing, bio.tools
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