README.md

benchmarking/BLR-RM-CEN/workflow/Snakefile

benchmarking/BLR-RM-CEN/workflow/run_Snakemake.sh

benchmarking/bench_BLR-RM-x-S2/workflow/Snakefile

...rking/bench_BLR-RM-x-S2/workflow/scripts/updateChunkID.py

benchmarking/bench_BLR-x-S2/workflow/Snakefile

benchmarking/bench_RM-x/workflow/Snakefile

benchmarking/bench_RM-x/workflow/run_Snakemake.sh

benchmarking/scripts/CENmap2align.py

benchmarking/scripts/RMcat2align.py

benchmarking/scripts/UpdateScoreOfMatches.py

benchmarking/scripts/launchCensor.py

benchmarking/scripts/updateChunkID.py

config/config.yaml

containers/how_install_te-finder.txt

containers/te_finder_2.31.sif

data/README.txt

data/gff/TEannotSnakemake_AthaGenome_ColO_refTEs_S0.gff3

data/gff/TEannotSnakemake_AthaGenome_athaTEref_ru_S0.gff3

data/gff/TEannotSnakemake_AthaGenome_athaTEref_ru_S1.gff3