| 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 |