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)…
☆59Mar 29, 2023Updated 3 years ago
Alternatives and similar repositories for dnaPipeTE
Users that are interested in dnaPipeTE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- GAPPadder is tool for closing gaps on draft genomes with short sequencing data☆28Jun 1, 2017Updated 9 years ago
- Repetitive motif detection by Assembly of Repetitive K-mers. RepARK is free for academic and non-profit use. By downloading you agree wit…☆16Sep 16, 2024Updated last year
- Python wrappers for programs that search for transposable elements☆19Jul 12, 2016Updated 9 years ago
- A tool to construct repeats directly from raw reads☆17May 29, 2021Updated 5 years ago
- Estimating repeat spectra and genome length from low-coverage genome skims☆12Aug 6, 2023Updated 2 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Reduction of Althaps and Duplicate Contigs for Improved Downstream Analysis☆20Apr 10, 2026Updated 2 months ago
- PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)☆20Nov 10, 2024Updated last year
- Few scripts facilitating the extraction of info from Repeat Masker .out files☆87May 25, 2021Updated 5 years ago
- source code of the paper "RepLong - de novo repeat discovery from long reads"☆17Jan 4, 2025Updated last year
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆25Apr 13, 2020Updated 6 years ago
- Domain based annotation of transposable elements☆23Oct 8, 2025Updated 8 months ago
- FamDB file format library and utilities☆43Jun 1, 2026Updated last week
- Improvement of Long Read Assemblies (ILRA) is a pipeline to help in the post assembly process (finishing) by cleaning and merging contigs…☆13Apr 21, 2026Updated last month
- A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.☆95Nov 23, 2024Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- meta-pipeline for repetitive element de-fragmentation and annotation☆28Oct 1, 2020Updated 5 years ago
- A loose collection of scripts and utilities for processing and analyzing the Goat reference genome assembly☆11Feb 28, 2017Updated 9 years ago
- TELR is a fast non-reference transposable element detector from long read sequencing data.☆35Jul 27, 2023Updated 2 years ago
- De-Novo Repeat Discovery Tool☆240Updated this week
- Earl Grey: A fully automated TE curation and annotation pipeline☆209Jun 2, 2026Updated last week
- Extensive de-novo TE Annotator☆448May 12, 2026Updated 3 weeks ago
- TransposonUltimate - a holistic set of tools for transposon identification☆86Mar 4, 2022Updated 4 years ago
- Tools for working with second gen assemblies, fasta sequences, etc☆95Sep 8, 2016Updated 9 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆216May 12, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A quick user guide for de novo transposable element (TE) library generation and TE screening. Utilising; the Extensive de novo TE Annotat…☆27Dec 7, 2022Updated 3 years ago
- Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequenc…☆39Jul 11, 2025Updated 11 months ago
- A tool for discovering transposable elements and describing patterns of genome evolution☆31Apr 23, 2023Updated 3 years ago
- R package to draw syntenic plots in 3 different styles☆46Feb 2, 2026Updated 4 months ago
- A Hi-C scaffolding method☆22Dec 22, 2021Updated 4 years ago
- ☆28Apr 21, 2026Updated last month
- Haplotype-aware genome assembly toolkit☆30Jan 8, 2020Updated 6 years ago
- SRF: Satellite Repeat Finder☆104Jan 8, 2024Updated 2 years ago
- Script to help assessing the evolutionary history of a TE family☆16Sep 5, 2019Updated 6 years ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- The MafFilter genome alignment processor☆19Apr 10, 2026Updated 2 months ago
- TSEBRA: Transcript Selector for BRAKER☆50Apr 7, 2026Updated 2 months ago
- BUSCOMP: BUSCO Compiler and Comparison tool☆21Sep 19, 2024Updated last year
- haplotypic duplication identification tool☆288Oct 30, 2025Updated 7 months ago
- finshingTool☆54Nov 22, 2016Updated 9 years ago
- Accompanying repository for our publications on manual curation methods for Transposable Elements.☆24Jun 26, 2024Updated last year
- ⛓ Long Interval Nucleotide K-mer Scaffolder☆73Jun 4, 2026Updated last week