A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

BMC Bioinformatics

Table 1 Short-read mapping tools

Name	Mapping Strategy	Indels Support	Quality evalutation	GPU-based
Barracuda	BWT-based indexing of the reference	Yes	Yes	Yes
BWA	BWT-based indexing of the reference	Yes	Yes	No
Bowtie	BWT-based indexing of the reference	No	Yes	No
CUHSHAW2	BWT-based indexing of the reference	Yes	Yes	Yes
CloudBurst	Hash the reads	Yes	No	No
MAQ	Hash the reads	No	Yes	No
RMAP	Hash the reads	Yes	Yes	No
SHRiMP2	Hash the reads	Yes	Yes	No
SOAP2	BWT-based indexing of the reference	Yes	Yes	No
SOAP3	BWT-based indexing of the reference	No	No	Yes
SOAP3-dp	BWT-based indexing of the reference	Yes	No	Yes

ISSN: 1471-2105