Searched almost all the day and only found 1 candidate that could match bowite a little bit. Im trying to find a short sequence aligner (illumina data set in fasta format) that allows gaps up to a maximum of 5 with or without mismatches. Bowtie only handles a few mismatches and no gaps, i found genomemapper but the output file is not .sam and i only know tablet for visualisation.
Thus my question is does someone knows an easy to handle short sequence aligner to a reference sequence that allows gaps/mismatches and export into a .sam format?
thanks!
Thus my question is does someone knows an easy to handle short sequence aligner to a reference sequence that allows gaps/mismatches and export into a .sam format?
thanks!
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