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Transposons mobility in M. incognita (INRA - Institut National de la Recherche Agronomique)
REPETpostAnal-V1.0.5.py
Version 2.0
File Citation
Kozlowski, Djampa, 2020, "REPETpostAnal-V1.0.5.py", Transposable Elements prediction and annotation in the M. incognita genome, https://doi.org/10.15454/EPTDOS/4WQ8LI, Portail Data INRAE, V2

This file is part of "Transposable Elements prediction and annotation in the M. incognita genome".

Dataset Citation
Kozlowski, Djampa, 2020, "Transposable Elements prediction and annotation in the M. incognita genome", https://doi.org/10.15454/EPTDOS, Portail Data INRAE, V2
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doi:10.15454/EPTDOS/4WQ8LI

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a7a5d1e82e1ba7c3f5730ebd8ce5ea7a
2020-07-03
29.5 KB
text/x-python
In-house python (>= 3) script. Used to parse REPET draft annotation (repeatome) and isolate canonical TE annotations.Requires as input i) REPET draft TE-annotation output (.gff3), ii) the TE-consensus library used for the annotation, iii) the genome fasta file. Default parameters are set for stringent filtering post-processing (e.g canonical TE-annotations). External Dependencies: bedtools (>= 2), blast+, bash. Required python libraries: subprocess, os, sys, re, pandas, argparse, numpy, Bio (SeqIO).
2020-07-03
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