| Authors(s) | Goubert C., Modolo L., Vieira C., Valiente Moro C., Mavingui P. and Boulesteix M. |
| Developer(s) | Clément Goubert and Laurent Modolo |
| Written in | Python3, bash, R |
| Operating System | Unix |
| Platform | x86-64 |
| Stable Release | 1.3 (2017) |
| Initial Release | 2015 |
| License | GNU Lesser General Public 2.1 |
| Website | GitHub |
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X per run).
Features
- Automatized analysis of TE from raw short-read data (typically genomic Illumina, single or paired-end)
- Reference-free assembly of TE with Trinity (repurposed RNA-seq assembler)
- TE classification using homology database (can be specified by the user)
- TE quantification using low coverage samples of the dataset (< 1X needed per library)
- TE landscapes analysis (approximation of the relative age of TE families)
See also
RepeatExplorer, AAARF (Assisted Automated Assembler of Repeat Families), RepARK
References
| 1. Goubert C., Modolo L., Vieira C., Valiente Moro C., Mavingui P and Boulesteix M.(2015) De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti) |