TEtools

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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]

Example:

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