hapsembler¶

Description¶

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 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.

Environment Variables¶

HPC_HAPSEMBLER_DIR - installation directory
HPC_HAPSEMBLER_BIN - executable directory
HPC_HAPSEMBLER_DOC - documentation directory
HPC_HAPSEMBLER_EX - examples directory

Citation¶

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

Categories¶

biology, assembly