TEtools

Description

Dfam TE Tools includes RepeatMasker, RepeatModeler, and coseg.

License

CC0 1.0 Universal

Usage

TE Tools software is distributed as Singularity image placed in /cvmfs/singularity.metacentrum.cz/TE-Tools/TE-tools-1.4.sif. No module load step is required.

singularity run /cvmfs/singularity.metacentrum.cz/TE-Tools/TE-tools-1.4.sif [command] [parameter]

Manual page:

singularity run /cvmfs/singularity.metacentrum.cz/TE-Tools/TE-tools-1.4.sif BuildDatabase -h

Example:

Directory with input data ($SCRATCHDIR) needs be linked with the image by -B option. Additionaly, specify full path to that file.

cp input_fasta_file.fa $SCRATCHDIR
cd $SCRATCHDIR
singularity run -B $SCRATCHDIR /cvmfs/singularity.metacentrum.cz/TE-Tools/TE-tools-1.4.sif BuildDatabase -name my_db_name $SCRATCHDIR/input_fasta_file.fa

Included software

The following software is included in the Dfam TE Tools container (version 1.4):

Software name	Included Version
RepeatModeler RepeatMasker coseg RMBlast HMMER TRF RepeatScout RECON cd-hit genometools LTR_retriever MAFFT NINJA UCSC utilities	2.0.2 4.1.2-p1 0.2.2 2.11.0 3.3.2 4.09.1 1.0.6 1.08 4.8.1 1.6.0 2.9.0 7.471 0.97-cluster_only v413

Documentation

https://github.com/Dfam-consortium/TETools

Homepage

https://github.com/Dfam-consortium/TETools