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Update README.md
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amvarani authored Oct 31, 2022
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Expand Up @@ -28,7 +28,7 @@ Since this pipeline can retrieve complete CRM elements, it is also possible to f
- All annotation follow the Rexdb and GyDB nomenclature as proposed by ``Orozco-Arias et al., 2019``.
- Proper soft-masking for downstream analysis (for structural gene annotation).
- Complete TE distribution Report (text file - a graphical version will be added).
- Identification of potential telomeric regions of each chromosome.
- Identification of potential (peri)centromeric regions of each chromosome.
- Drawing of the Repeat Landscape.
- LTR Age Ploting using R (Gypsy and Copia).

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- Global TE annotation with a modified version of EDTA pipeline (including all dependencies) tailored for non-model plant genomes and to remove potential false positive predictions: https://github.com/oushujun/EDTA.
- TE annotation and validation with TEsorter: https://github.com/zhangrengang/TEsorter
- Global TE report based on a modified version of ProcessRepeats scripts from RepeatMasker: https://www.repeatmasker.org/RepeatMasker/
- Repeat Landscape and LTR Age Ploting using RepeatMasker and R scripts. **to be added**
- Repeat Landscape and LTR Age Ploting using RepeatMasker and R scripts.

## Installation

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