Pinned Repositories
GraffiTE
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
consensus2genome
[DEPRECATED] R function that blast any TE consensus to reference genome and output mapping graph
dnaPipeTE
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).
dnaPT_utils
A collection of scripts to perform several downstream analyses with dnaPipeTE 1.3
rm2gff3
Convert RepeatMasker ".out" file into a gff3 with colors!!!
So2
So2 TE Bioinformatic ressources -- Parisot et al. 2020
TE-Aid
Annotation helper tool for the manual curation of transposable element consensus sequences
typeref
Bi-allelic genotyping of reference transposable elements
TypeTE
Genotyping of segregating mobile elements insertions
clemgoub's Repositories
clemgoub/dnaPipeTE
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).
clemgoub/TE-Aid
Annotation helper tool for the manual curation of transposable element consensus sequences
clemgoub/rm2gff3
Convert RepeatMasker ".out" file into a gff3 with colors!!!
clemgoub/TypeTE
Genotyping of segregating mobile elements insertions
clemgoub/dnaPT_utils
A collection of scripts to perform several downstream analyses with dnaPipeTE 1.3
clemgoub/consensus2genome
[DEPRECATED] R function that blast any TE consensus to reference genome and output mapping graph
clemgoub/So2
So2 TE Bioinformatic ressources -- Parisot et al. 2020
clemgoub/typeref
Bi-allelic genotyping of reference transposable elements
clemgoub/dnaPipeTE2
clemgoub/eager
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
clemgoub/denovoTE-eval
Supporting repository for article "Software Evaluation for 'de novo' Detection of Transposons"
clemgoub/FraHMMER
Frameshift Aware Translated Alignments
clemgoub/LIONS
LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
clemgoub/pMEsim
polymorphic mobile element simulator
clemgoub/REPCLASS
This tool facilitates transposable elements consensus classification
clemgoub/RPi_GPIO_basics
Basics GPIO projects for Raspberry Pi
clemgoub/TD_albo
Suite of scripts used for the production of Transposable Elements polymorphism (High-Throughput Transposon Display) data in 140 individuals of Aedes albopictus. Used in Goubert et al. bioRxiv: https://doi.org/10.1101/049197