Difference between revisions of "Reptile"

From UFRC
Jump to navigation Jump to search
m (Text replace - "<!--Location--> {{App_Location|app={{#var:app}}|{{#var:ver}}}}" to "")
 
(12 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
 
__NOEDITSECTION__
 
__NOEDITSECTION__
[[Category:Software]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Math]]
<!-- ########  Template Configuration ######## -->
+
{|<!--Main settings - REQUIRED-->
<!--Edit definitions of the variables used in template calls
 
Required variables:
 
app - lowercase name of the application e.g. "amber"
 
url - url of the software page (project, company product, etc) - e.g. "http://ambermd.org/"
 
Optional variables:
 
INTEL - Version of the Intel Compiler e.g. "11.1"
 
MPI - MPI Implementation and version e.g. "openmpi/1.3.4"
 
-->
 
{|
 
<!--Main settings - REQUIRED-->
 
 
|{{#vardefine:app|reptile}}
 
|{{#vardefine:app|reptile}}
 
|{{#vardefine:url|http://aluru-sun.ece.iastate.edu/doku.php?id=reptile}}
 
|{{#vardefine:url|http://aluru-sun.ece.iastate.edu/doku.php?id=reptile}}
<!--Compiler and MPI settings - OPTIONAL -->
 
|{{#vardefine:intel|}} <!-- E.g. "11.1" -->
 
|{{#vardefine:mpi|}} <!-- E.g. "openmpi/1.3.4" -->
 
<!--Choose sections to enable - OPTIONAL-->
 
|{{#vardefine:mod|1}} <!--Present instructions for running the software with modules -->
 
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:exe|1}} <!--Present manual instructions for running the software -->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
 
|{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF-->
Line 42: Line 27:
  
 
[http://aluru-sun.ece.iastate.edu/doku.php?id=reptile Upstream documentation] for {{#var:app}}.
 
[http://aluru-sun.ece.iastate.edu/doku.php?id=reptile Upstream documentation] for {{#var:app}}.
 
+
<!--Modules-->
==Available Versions==
+
==Environment Modules==
* 1.1 (serial, and parallelized OMP and Intel/OMP versions)
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
{{#if: {{#var: mod}}|==Running the application using modules==
+
==System Variables==
{{App_Module|app={{#var:app}}|intel={{#var:intel}}|mpi={{#var:mpi}}}}|}}
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_REPTILE_BIN - Executable directory
 
* HPC_REPTILE_BIN - Executable directory
 
* HPC_REPTILE_CONF - Sample configuration files
 
* HPC_REPTILE_CONF - Sample configuration files
{{#if: {{#var: exe}}|==How To Run==
+
<!--Additional-->
 +
{{#if: {{#var: exe}}|==Additional Information==
 
Make sure that the environmental variable <code>OMP_NUM_THREADS</code> is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary.
 
Make sure that the environmental variable <code>OMP_NUM_THREADS</code> is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary.
  
Line 65: Line 51:
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
{{#if: {{#var: pbs}}|==PBS Script Examples==
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
 
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}}
{{#if: {{#var: policy}}|==Usage policy==
+
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used)
 
|}}
 
|}}

Latest revision as of 21:46, 21 August 2022

Description

reptile website  

Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. Reptile has several favorable properties:

  • Memory efficiency. Reptile can process input data with sizes larger than main memory. For instance, to process a 160x coverage (3.8GB) Illumina data for E. coli it requires only ~1GB memory, which is easily available in a desktop computer.
  • High speed. Processing Illumina data for a microbe typically takes 0.5hr ~ 2hrs, depending on the number and the quality of reads.
  • Can handle reads containing non-acgt characters and reads with non-equal length.
  • Makes simple use of quality score information.
  • Reptile has been developed by Xiao Yang, Karin Dorman and Srinivas Aluru.

Upstream documentation for reptile.

Environment Modules

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

System Variables

  • HPC_REPTILE_DIR - installation directory
  • HPC_REPTILE_BIN - Executable directory
  • HPC_REPTILE_CONF - Sample configuration files

Additional Information

Make sure that the environmental variable OMP_NUM_THREADS is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary.

There is a reptile tutorial written by Daniel S. Standage.

The available binaries and scripts include:

fastq-converter reptile_merger reptile-omp reptile-omp-intel reptile-v1.1 seq-analy.

Sample configuration files are in $HPC_REPTILE_CONF



Citation

If you publish research that uses reptile you have to cite it as follows: X. Yang, K. Dorman and S. Aluru, “Reptile: Representative tiling for short read error correction”, Bioinformatics, 26(20), 2526-2533, 2010.