Earl Grey: A fully automated TE curation and annotation pipeline
☆199Mar 12, 2026Updated last week
Alternatives and similar repositories for EarlGrey
Users that are interested in EarlGrey are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Extensive de-novo TE Annotator☆435Mar 12, 2026Updated last week
- TEtrimmer: a novel tool to automate manual curation of transposable elements☆113Feb 26, 2026Updated 3 weeks ago
- Few scripts facilitating the extraction of info from Repeat Masker .out files☆84May 25, 2021Updated 4 years ago
- GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered …☆240Mar 4, 2026Updated 2 weeks ago
- High-precision TE Annotator☆151Dec 4, 2025Updated 3 months ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆205Nov 23, 2025Updated 4 months ago
- meta-pipeline for repetitive element de-fragmentation and annotation☆28Oct 1, 2020Updated 5 years ago
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆148Jan 27, 2025Updated last year
- haplotypic duplication identification tool☆277Oct 30, 2025Updated 4 months ago
- Mabs, a genome assembly tool that optimizes parameters of Hifiasm and Flye☆35Mar 5, 2026Updated 2 weeks ago
- ☆41Jun 8, 2023Updated 2 years ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆561Feb 14, 2024Updated 2 years ago
- ☆237Jan 24, 2025Updated last year
- Snakemake pipeline to analyze transposable element 'omics data.☆32Mar 5, 2026Updated 2 weeks ago
- Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation☆183Dec 16, 2025Updated 3 months ago
- MCHelper: An automatic tool to curate transposable element libraries☆45Jul 3, 2025Updated 8 months ago
- This is the standalone version of the EviAnn pipeline☆142Mar 13, 2026Updated last week
- Tool to plot synteny and structural rearrangements between genomes☆343Apr 7, 2025Updated 11 months ago
- A genome completeness evaluation tool based on miniprot☆237Sep 18, 2025Updated 6 months ago
- Inpactor2: LTR retrotransposon detector and classificator using Deep Learning☆28Jun 17, 2025Updated 9 months ago
- Annotation helper tool for the manual curation of transposable element consensus sequences☆54Mar 5, 2025Updated last year
- oxford dot plots☆166Feb 17, 2026Updated last month
- a UNIX shell toolkit for processing and analyzing multiple sequence alignments and phylogenies☆82Updated this week
- Portable solution to generate genome alignment chains using lastz☆61Dec 20, 2025Updated 3 months ago
- An accurate GFF3/GTF lift over pipeline☆531Aug 1, 2023Updated 2 years ago
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆451Oct 20, 2025Updated 5 months ago
- dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify T…☆60Mar 29, 2023Updated 2 years ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214Mar 9, 2026Updated 2 weeks ago
- A program for assessing the T2T genome continuity☆92Feb 28, 2026Updated 3 weeks ago
- We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …☆33Jan 3, 2022Updated 4 years ago
- Synteny and Rearrangement Identifier☆454Mar 17, 2026Updated last week
- Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)☆373Feb 13, 2025Updated last year
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Feb 25, 2026Updated last month
- Neural network classification of TE☆97Oct 9, 2025Updated 5 months ago
- A pipeline to detect chimeric transcripts derived from genes and transposable elements.☆36Jul 27, 2025Updated 7 months ago
- Accompanying repository for our publications on manual curation methods for Transposable Elements.☆21Jun 26, 2024Updated last year
- Meta-pipeline to identify transposable element insertions using next generation sequencing data☆105May 31, 2025Updated 9 months ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆121Feb 12, 2026Updated last month
- Minimizer-based assembly scaffolding and mapping using long reads☆49Mar 10, 2026Updated 2 weeks ago