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Table 3 Feature comparison of BOAT and other commonly used Solexa read mapping programs

From: BOAT: Basic Oligonucleotide Alignment Tool

  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
  1. * 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.