BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
☆450Oct 20, 2025Updated 4 months ago
Alternatives and similar repositories for BRAKER
Users that are interested in BRAKER are comparing it to the libraries listed below
Sorting:
- Genome annotation with AUGUSTUS☆328Aug 15, 2025Updated 6 months ago
- TSEBRA: Transcript Selector for BRAKER☆49Nov 14, 2025Updated 3 months 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
- Tools for fast and flexible genome assembly scaffolding and improvement☆559Feb 14, 2024Updated 2 years ago
- Extensive de-novo TE Annotator☆430Updated this week
- k-mer based assembly evaluation☆339Jun 28, 2024Updated last year
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆744Mar 18, 2025Updated 11 months ago
- De-Novo Repeat Discovery Tool☆231Jul 21, 2025Updated 7 months ago
- source code for EVM☆122Nov 29, 2024Updated last year
- Protein hint generation pipeline for gene finding in eukaryotic genomes☆60Oct 27, 2023Updated 2 years ago
- Synteny and Rearrangement Identifier☆448Apr 29, 2025Updated 10 months ago
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- An accurate GFF3/GTF lift over pipeline☆530Aug 1, 2023Updated 2 years ago
- Official home of genome aligner based upon notion of Cactus graphs☆658Feb 24, 2026Updated last week
- Eukaryotic Genome Annotation Pipeline☆382Feb 12, 2026Updated 3 weeks ago
- Python library to facilitate genome assembly, annotation, and comparative genomics☆890Mar 2, 2026Updated last week
- Version 5 of the CAFE phylogenetics software☆161Feb 12, 2025Updated last year
- Fast and accurate de novo assembler for long reads☆398May 10, 2024Updated last year
- haplotypic duplication identification tool☆275Oct 30, 2025Updated 4 months ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆207Nov 18, 2022Updated 3 years ago
- PASA software☆198Feb 12, 2025Updated last year
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆563Jan 13, 2026Updated last month
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆174May 30, 2021Updated 4 years ago
- Fast and accurately polish the genome generated by long reads.☆240Jan 9, 2025Updated last year
- Phylogenetic orthology inference for comparative genomics☆839Jul 15, 2025Updated 7 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆254Jan 5, 2026Updated 2 months ago
- Generate an interactive dot plot from mummer or minimap alignments☆212Jan 17, 2024Updated 2 years ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆383Feb 24, 2026Updated last week
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆215Updated this week
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆178Oct 20, 2024Updated last year
- Tool to plot synteny and structural rearrangements between genomes☆343Apr 7, 2025Updated 11 months ago
- Yet another Hi-C scaffolding tool☆172Nov 4, 2024Updated last year
- 3D de novo assembly (3D DNA) pipeline☆223Nov 29, 2023Updated 2 years ago
- Fast genome analysis from unassembled short reads☆313Apr 8, 2024Updated last year
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆204Nov 23, 2025Updated 3 months ago
- Using Deep Learning to predict gene annotations☆277Updated this week
- Mummer alignment tool☆550Feb 4, 2025Updated last year
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆159Nov 4, 2025Updated 4 months ago