Table 3

Feature comparison of BOAT and other commonly used Solexa read mapping programs

Maximum number of mismatches allowed

Gapped alignment

Trimming alignment

BLAST-style E-value

Pair-end reads

SNP Calling


BOAT

No hardcoded limitation

YES

YES

YES

YES

YES

RMAP

No hardcoded limitation

NO

NO

NO

NO

NO

MAQ

3

NO

NO

NO

YES

YES

SOAP

5

NO

YES*

NO

YES

NO

SeqMap

5

YES

NO

NO

NO

NO


* SOAP provided a similar mode called "iterative alignment" by iteratively trimming base pairs at the 3'-end and redoing the alignment until hits are detected or the remaining sequence is too short.

Zhao et al. BMC Genomics 2009 10(Suppl 3):S2   doi:10.1186/1471-2164-10-S3-S2

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