Difference between revisions of "Hapsembler"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|hapsembler}} |{{#vardefine:url|http://compbio.cs.toronto.ed...") |
|||
(5 intermediate revisions by 3 users not shown) | |||
Line 1: | Line 1: | ||
− | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Assembly]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|hapsembler}} | |{{#vardefine:app|hapsembler}} | ||
Line 10: | Line 10: | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
− | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
Line 25: | Line 25: | ||
#scaffolding | #scaffolding | ||
<!--Modules--> | <!--Modules--> | ||
− | == | + | ==Environment Modules== |
− | < | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
==System Variables== | ==System Variables== | ||
− | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Line 65: | Line 55: | ||
{{#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: | ||
− | + | ||
+ | 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 | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> |
Latest revision as of 18:15, 15 August 2022
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
Environment Modules
Run module spider hapsembler
to find out what environment modules are available for this application.
System Variables
- HPC_HAPSEMBLER_DIR - installation 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