HapCol implements a fixed-parameter algorithm for the k-constrained Minimum Error Correction problem (k-cMEC), a variant of the well-known MEC problem where the maximum number of corrections per column is bounded by an integer k. HapCol, while is as accurate as other exact state-of-the-art combinatorial approaches, is significantly faster and more memory-efficient than them. Moreover, HapCol is able to process datasets composed of both long reads (over 100 000bp long) and coverages up to 25x on standard workstations/small servers, whereas the other approaches cannot handle long reads or coverages greater than 20x.
- Linux / MacOsX
- gcc, make
:: MORE INFORMATION
HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads.
Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P.
Bioinformatics. 2015 Aug 26. pii: btv495