(latest version of hapsembler)

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If you would like to be notified of new releases of hapsembler please send an email to: hapsembler[at]cs[dot]toronto[dot]edu with the subject line "subscribe" and we will add you to our mailing list.

Looking for a read correction tool or a scaffolder?

You can now download the error correction module Encore or our in-house stand-alone scaffolder Scarpa separately from Hapsembler. Just follow the links on the left.

What is Hapsembler?

Hapsembler is a haplotype-specific genome assembly toolkit that is designed for genomes that are rich in SNPs and other types of polymorphism. Hapsembler can be used to assemble reads from a variety of platforms including Illumina and Roche/454. Hapsembler is available free of charge for academic and commercial use under the GNU General Public License (GPL).

To cite Hapsembler and Encore:

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.

To cite Scarpa:

Nilgun Donmez and Michael Brudno (2013) Scarpa: Scaffolding reads with practical algorithms, Bioinformatics, 29 (2013), 428-434