Difference between revisions of "HybPiper"

From UFRC
Jump to navigation Jump to search
 
(One intermediate revision by one other user not shown)
Line 21: Line 21:
  
 
<!--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_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
* HPC_{{#uppercase:{{#var:app}}}}_DOC - documentation directory
+
* HPC_{{uc:{{#var:app}}}}_DOC - documentation directory
* HPC_{{#uppercase:{{#var:app}}}}_EXE - example directory
+
* HPC_{{uc:{{#var:app}}}}_EXE - example directory
  
 
<!--Configuration-->
 
<!--Configuration-->

Latest revision as of 18:36, 10 June 2022

Description

hybpiper website  

HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads.

Environment Modules

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

System Variables

  • HPC_HYBPIPER_DIR - installation directory
  • HPC_HYBPIPER_BIN - executable directory
  • HPC_HYBPIPER_DOC - documentation directory
  • HPC_HYBPIPER_EXE - example directory




Citation

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

Johnson, M. G., Gardner, E. M., Liu, Y., Medina, R., Goffinet, B., Shaw, A. J., Zerega, N. J. C, and Wickett, N. J. (2016). HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment. Applications in Plant Sciences, 4(7), 1600016. doi:10.3732/apps.1600016