Encore is a sequencing error correction tool that is designed for highly polymorphic genome sequencing projects. It can be used as a preprocessing tool for de novo assembly or as a read correction tool for any other purpose. It supports multiple NGS platforms and is suitable for low-polymorphism datasets as well as datasets with high SNP and micro-indel rates.
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Nilgun Donmez and Michael Brudno (2011)
Hapsembler: an assembler for highly polymorphic genomes.
In Proceedings of the 15th Annual international conference on Research in computational molecular biology (RECOMB’11), Springer-Verlag, Berlin, Heidelberg, 38-52.