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Resource Name
SSAHASNP
RRID:SCR_009415 RRID Copied      
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SSAHASNP (RRID:SCR_009415)
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Resource Information

URL: http://www.sanger.ac.uk/science/tools/ssahasnp-0

Proper Citation: SSAHASNP (RRID:SCR_009415)

Description: A polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence. (entry from Genetic Analysis Software)

Abbreviations: SSAHASNP

Synonyms: Sequence Search and Alignment by Hashing Algorithm for SNP detection

Resource Type: software resource, software application

Keywords: gene, genetic, genomic

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