LOCAS / SUPERLOCAS
LOCAS is a programm to assemble short reads of second generation sequencing technologies. It explicitly handles low coverage data by allowing mismatches in the overlap alignment of reads.
SUPERLOCAS provides some additional features for resequencing projects. In a resequencing project reads are mapped onto a closely related reference genome and a consensus from the mapped reads is calculated as an approximation of the new genome sequence. (Highly polymorphic regions and insert sites are not covered with this consenus.) SUPERLOCAS can be used to incorporate unmapped reads into the assembly of mapped regions and elongate this consenus. Further, SUPERLOCAS takes advantage of given mapping positions of reads.
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