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Table 1 Short-read mapping tools

From: A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

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
  1. A summary of some of the most popular short-read mapping tools.