Pairwise whole genome aligner

Generate a Transposable Elements library from a FastGA whole genome alignment.

pipeline to identify and annotate soloLTR sequences

Reference-free profiling of polyploid genomes

TEtrimmer: a novel tool to automate manual curation of transposable elements

Nextflow script for running RepeatMasker on a cluster

Windows inside a Docker container.

MMseqs2: ultra fast and sensitive search and clustering suite

Curated list of awesome GPTs 👍.

The Unix Shell

Earl Grey: A fully automated TE curation and annotation pipeline

Peak calling for ATAC-seq data using contrastive learning on biological replicates

Domain based annotation of transposable elements

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Chris Titus Tech's Windows Utility - Install Programs, Tweaks, Fixes, and Updates

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

SPAdes Genome Assembler

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.

hybrid assembly pipeline for bacterial genomes

ecc_caller is a pipeline designed to take Illumina NovaSeq paired end sequencing reads generated from isolated circular DNA and call eccDNA forming regions.

Leading to the dataviz you need

Inpactor2: LTR retrotransposon detector and classificator using Deep Learning

Ultra-fast and memory-efficient (meta-)genome assembler

MCHelper: An automatic tool to curate transposable element libraries

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.