TEPID

From MetaCentrum
Jump to navigation Jump to search

Description

Transposable element polymorphism identification. Available is version fixed by Rimjhim Roy Choudhury solving plenty of problems with the original version.

Licence

GNU GPL v3

Use

Load module tepid-fix (it loads Python 2 modules) and required tools (Bedtools, Bowtie 2, Samblaster, SAMtools and Yaha) and use TEPID:

# Load TEPID
module add tepid-fix
# tepid-map requires bowtie2, samblaster (only for paired-end data), samtools and yaha
module add bowtie2-2.3.0
module add samblaster-0.1.24 # Only for paired-end data
module add samtools-1.9
module add yaha-0.1.83
tepid-map
tepid-map-se
# tepid-discover and tepid-refine require bedtools
module add bedtools-2.26.0
tepid-discover
tepid-refine

Documentation

https://github.com/ListerLab/TEPID/blob/master/README.md and https://github.com/rimjhimroy/TEPID-fix/blob/master/README.md

Program manager

meta@cesnet.cz

Homepage

https://github.com/ListerLab/TEPID and https://github.com/rimjhimroy/TEPID-fix