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