Resources

URL

Ref

MAQ

http://maq.sourceforge.net/

[33]

SOAPaligner/soap2

http://soap.genomics.org.cn/index.html

[36]

Bowtie

http://bowtie-bio.sourceforge.net/index.shtml

[32]

BLAT

http://genome.ucsc.edu/cgi-bin/hgBlat

[79]

BWA

http://maq.sourceforge.net/

[80]

BFAST

http://bfast.sourceforge.net

[81]

SHRiMP

http://compbio.cs.toronto.edu/shrimp.

[82]
SOAP, Short Oligonucleotide Analysis Package; MAQ, Mapping and Assembly with Quality; BLAT, BLAST-like alignment tool, BWA, Burrows-Wheeler Alignment; BFAST, BLAT-like Fast Accurate Search Tool; SHRiMP, The Short-Read Mapping Package.
Table 2: Alignment tools for short reads.