Extensive de-novo TE Annotator

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

De-Novo Repeat Discovery Tool

Genome Assembly and Annotation Service code

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

Dfam Transposable Element Tools Docker container.

⛓ Long Interval Nucleotide K-mer Scaffolder

A parallel wrapper for LTR_FINDER

use long sequenced reads to close gaps in assemblies

A toolkit for annotation of transposable element families from unassembled sequence reads

🚝RAILS and 👞🔨Cobbler: Assembly Improvement by Long Sequence Scaffolding/Gap-filling

TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data

Code that was used in the Assemblathon 1 and 2 projects