RepeatModeler 2016

Introduction

RepeatModeler (by Robert Hubley and Arian Smit) is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. ¹

Installed version(s)

This version is installed on... environment hpc-env/6.4:

RepeatModeler/1.0.11-foss-2017b

environment hpc-env/8.3:

RepeatModeler/2.0.2a-foss-2019b

Using RepeatModeler

If you want to find out more about RepeatModeler on the HPC Cluster, you can use the command

module spider RepeatModeler

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env/8.3
module load RepeatModeler

Always remember: this command is case sensitive!

When using RepeatModeler's help function, this will show up:

NAME
   RepeatModeler - Model repetitive DNA

SYNOPSIS
     RepeatModeler [-options] -database <XDF Database>

DESCRIPTION
   The options are:

   -h(elp)
       Detailed help

   -database
       The prefix name of a XDF formatted sequence database containing the
       genomic sequence to use when building repeat models. The database
       may be created with the WUBlast "xdformat" utility or with the
       RepeatModeler wrapper script "BuildXDFDatabase".

   -engine <abblast|wublast|ncbi>
       The name of the search engine we are using. I.e abblast/wublast or
       ncbi (rmblast version).

   -pa #
       Specify the number of shared-memory processors available to this
       program. RepeatModeler will use the processors to run BLAST searches
       in parallel. i.e on a machine with 10 cores one might use 1 core for
       the script and 9 cores for the BLAST searches by running with "-pa
       9".

   -recoverDir <Previous Output Directory>
       If a run fails in the middle of processing, it may be possible
       recover some results and continue where the previous run left off.
       Simply supply the output directory where the results of the failed
       run were saved and the program will attempt to recover and continue
       the run.

   -srand #
       Optionally set the seed of the random number generator to a known
       value before the batches are randomly selected ( using Fisher Yates
       Shuffling ). This is only useful if you need to reproduce the sample
       choice between runs. This should be an integer number.

Documentation

The full documentation can be found here.