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You can also configure other parameters.
Score for a match — maximum edit distance. An integer value should be input.Mismatch penalty — the fraction of missing alignments given 2% uniform base error rate. A float value is used (-a) — score of a match.
Mismatch penalty (-b) — mismatch penalty.
Gap open penalty — maximum number of gap opens(-q) — gap open penalty.
Gap extention penalty — algorithm for constructing BWT index(-r) — Gap extension penalty. The penalty for a contiguous gap of size k is q+k*r.
Band width (-w) - Band width in the banded alignment.
Mask level (-c) - Coefficient for threshold adjustment according to query length. Given an l-long query, the threshold for a hit to be retained is a*max{T,c*log(l)}.
Number of threads (-t) - Number of threads in the multi-threading mode.
Size of chunk of reads (-s) - Maximum SA interval size for initiating a seed. Higher -s increases accuracy at the cost of speed.
Score threshold (divided by much score) (-T) - minimum score threshold.
Z-best (-z) - Z-best heuristics. Higher -z increases accuracy at the cost of speed.
Number of seeds to start rev alignment (-N) - Minimum number of seeds supporting the resultant alignment to skip reverse alignment.
Prefer hard clipping in SAM output - (-H) - use hard clipping in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.
Select the required parameters and press the Start button.