Difference between revisions of "Bloomfiltertrie"
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(Created page with "Category:SoftwareCategory:Phylogenetics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|bloomfiltertrie}} |{{#vardefine:url|https://github.com/GuillaumeHolley/Bloom...") |
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | 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 |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
| Line 60: | Line 60: | ||
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: | ||
| − | @article{holley2016bft, | + | @article{holley2016bft, |
| − | + | title="{Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage}", | |
| − | + | author={Holley, Guillaume and Wittler, Roland and Stoye, Jens}, | |
| − | + | journal={Algorithms Mol. Biol.}, | |
| − | + | volume={11}, | |
| − | + | pages={3}, | |
| − | + | year={2016} | |
| − | } | + | } |
|}} | |}} | ||
Latest revision as of 21:18, 6 December 2019
Description
This repository contains the source code of the Bloom Filter Trie (BFT) library. The BFT is an alignment-free, reference-free and incremental succinct data structure for colored de Bruijn graphs. It is based on the burst trie and use Bloom filters for efficient trie and graph traversals. The data structure indexes k-mers and their colors based on a new representation of trie vertices that compress and index shared substrings. A typical application of the BFT is pan-genome indexing.
Environment Modules
Run module spider bloomfiltertrie to find out what environment modules are available for this application.
System Variables
- HPC_BLOOMFILTERTRIE_DIR - installation directory
- HPC_BLOOMFILTERTRIE_BIN - executable directory
Citation
If you publish research that uses bloomfiltertrie you have to cite it as follows:
@article{holley2016bft,
title="{Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage}",
author={Holley, Guillaume and Wittler, Roland and Stoye, Jens},
journal={Algorithms Mol. Biol.},
volume={11},
pages={3},
year={2016}
}