Difference between revisions of "Vamb"
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Johnbullard (talk | contribs) (Created page with "Category:Software Category:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|vamb}} |{{#vardefine:url|https://github.com/RasmussenLab/vamb}} <!--CONFIGURATION...") |
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==System Variables== | ==System Variables== | ||
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_BIN- executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 18:59, 1 February 2021
Description
Vamb is a metagenomic binner which feeds sequence composition information from a contig catalogue and co-abundance information from BAM files into a variational autoencoder and clusters the latent representation. It performs excellently with multiple samples, and pretty good on single-sample data. Vamb is implemented purely in Python (with a little bit of Cython) and can be used both from command line and from within a Python interpreter.
Environment Modules
Run module spider vamb to find out what environment modules are available for this application.
System Variables
- HPC_VAMB_DIR - installation directory
- HPC_VAMB_BIN- executable directory