BOAT: Basic Oligonucleotide Alignment Tool

BMC Genomics

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.

ISSN: 1471-2164