Difference between revisions of "BloomTree"

From UFRC
Jump to navigation Jump to search
 
(One intermediate revision by the same user not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Biology]][[Category:Phylogenetics]][[Category:Data Mining]]
+
[[Category:Software]][[Category:Data Mining]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|Bloomtree}}
 
|{{#vardefine:app|Bloomtree}}
Line 24: Line 24:
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
 
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
===Serial===
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory

Latest revision as of 16:49, 10 June 2022

Description

Bloomtree website  

The Sequence Bloom Tree (SBT) is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence. The code base provided here is an implementation of SBT written in C++ and is open source.

Environment Modules

Run module spider Bloomtree to find out what environment modules are available for this application.

System Variables

  • HPC_BLOOMTREE_DIR - installation directory




Citation

If you publish research that uses Bloomtree you have to cite it as follows:

Brad Solomon and Carl Kingsford. Fast search of thousands of short-read sequencing experiments. Nature biotechnology. 2016 doi: 10.1038/nbt.3442