Difference between revisions of "Hapsembler"
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
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| + | To cite Hapsembler and Encore: | ||
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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. | ||
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| + | To cite Scarpa: | ||
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| + | Nilgun Donmez and Michael Brudno (2013) Scarpa: Scaffolding reads with practical algorithms, Bioinformatics, 29 (2013), 428-434 | ||
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Revision as of 22:27, 23 July 2014
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 is described in contain three main stages:
- error correction
- genome assembly
- scaffolding
Required Modules
System Variables
- HPC_{{#uppercase: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