Hapler is a tool for assembling robust haplotype regions given alignments (from de-novo assembly or mapping to a reference) of genetically diverse sequence data. Hapler compares each sequence to every other, and groups sequences together into sets that don’t have any conflicts (minimum coloring of the sequence ‘conflict graph’). This can be done in O(n^3) time, because Hapler assumes that sequences contain no gaps (e.g., it ignores mate-pair information). Because such a minimum coloring is usually not unique, Hapler by default produces many pseudo-random colorings and only keeps haplotype groupings which are common to all. In practice this drastically increases the correctness of results.
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BMC Genomics. 2012 Apr 12;13 Suppl 2:S4. doi: 10.1186/1471-2164-13-S2-S4.
Haplotype and minimum-chimerism consensus determination using short sequence data.
O’Neil ST, Emrich SJ.