Extensive de-novo TE Annotator
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Updated
May 23, 2024 - Perl
Extensive de-novo TE Annotator
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
Earl Grey: A fully automated TE curation and annotation pipeline
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).
A pipeline for predicting and masking transposable elements in multiple genomes.
Nextflow workflow for automatic repeat detection, classification and masking
A toolkit for annotation of transposable element families from unassembled sequence reads
Annotation helper tool for the manual curation of transposable element consensus sequences
Database-Integrated Genome Screening (DIGS) tool. Explore the dark genome using BLAST and a relational database.
Transposon Insertion Finder - Detection of new TE insertions in NGS data
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
Distribution of TEs and their relationship to genes in host genome
A pipeline to detect chimeric transcripts derived from genes and transposable elements.
a GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data
A tool for discovering transposable elements and describing patterns of genome evolution
A suite of C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. A part of the REPET package.
starfish: a modular toolkit for giant mobile element annotation
code to analyse RepeatMasker output
SLURM-ready bash scripts to run the complete REPET pipeline
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