Hapsembler

Description

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

System Variables

• HPC_HAPSEMBLER_DIR

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

Validation

• Validated 4/5/2018