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VAAL is 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’. VAAL then deduces from that a list of differences between the sample and related genomes.
Alternatively, VAAL 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.
Alternatively, VAAL 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.
