SOFT : T-lex
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Site du soft: https://github.com/GonzalezLab/T-lex3
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LICENSE:
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GPLv3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/T-lex
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Load binaries and environment:
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-> Version v3.0 (60b7b0b)

For the Target Site Duplication (TSD) detection, you need Phrap version 1.090518. License is nominative. You must contact the original authors to get permission and install it yourself in your directory.
http://www.phrap.org/

Don't forget to export it in your PATH before use T-lex.
export PATH="path/to/phrap":$PATH

#Need Repeatmasker,SHRIMP2,Blat,samtools, bcftools, bwa; faxtX toolkit, FastaGrep 
module load bioinfo/RepeatMasker-4.1.0 bioinfo/SHRiMP_2_2_3 bioinfo/SHRiMP_2_2_3 bioinfo/kentUtils-v370 bioinfo/samtools-1.11 bioinfo/bcftools-1.11 bioinfo/bwa-0.7.17 bioinfo/fastx_toolkit-0.0.14 bioinfo/fastagrep-v2.0

module load bioinfo/T-lex-v3.0

Example directory for use on cluster:
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/usr/local/bioinfo/src/T-lex/example_on_cluster

To submit: sbatch test_T-lex-v3.0.sh (eerror sin example because of absence of phrap)

See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.