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hapsembler website  

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.

The Hapsembler pipeline is described in contain three main stages:

  1. error correction
  2. genome assembly
  3. scaffolding

Environment Modules

Run module spider hapsembler to find out what environment modules are available for this application.

System Variables

  • HPC_HAPSEMBLER_DIR - installation directory


If you publish research that uses hapsembler you have to cite it as follows:

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