Using Deep Learning to predict gene annotations
☆276Feb 25, 2026Updated this week
Alternatives and similar repositories for Helixer
Users that are interested in Helixer are comparing it to the libraries listed below
Sorting:
- 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
- This is the standalone version of the EviAnn pipeline☆139Feb 5, 2026Updated 3 weeks ago
- Tiberius is a deep learning gene finder.☆99Feb 19, 2026Updated last week
- Yet another Hi-C scaffolding tool☆172Nov 4, 2024Updated last year
- Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation☆181Dec 16, 2025Updated 2 months ago
- TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annot…☆203Nov 23, 2025Updated 3 months ago
- A genome completeness evaluation tool based on miniprot☆235Sep 18, 2025Updated 5 months ago
- Repeat-aware polishing genomes assembled using HiFi long reads☆98Nov 12, 2025Updated 3 months ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆254Jan 5, 2026Updated last month
- BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…☆449Oct 20, 2025Updated 4 months ago
- ☆89Dec 3, 2025Updated 3 months ago
- An accurate GFF3/GTF lift over pipeline☆530Aug 1, 2023Updated 2 years ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆233Sep 6, 2024Updated last year
- Align proteins to genomes with splicing and frameshift☆395Jan 5, 2026Updated last month
- High-precision TE Annotator☆151Dec 4, 2025Updated 2 months ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆382Updated this week
- Tool to plot synteny and structural rearrangements between genomes☆342Apr 7, 2025Updated 10 months ago
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆561Jan 13, 2026Updated last month
- Python library to facilitate genome assembly, annotation, and comparative genomics☆890Feb 15, 2026Updated 2 weeks ago
- Tools for fast and flexible genome assembly scaffolding and improvement☆558Feb 14, 2024Updated 2 years ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 2 years ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆167Oct 29, 2025Updated 4 months ago
- ☆119Oct 10, 2025Updated 4 months ago
- Extensive de-novo TE Annotator☆430Oct 12, 2025Updated 4 months ago
- A tool for performing collinearity-incorporating homology inference☆33Oct 7, 2023Updated 2 years ago
- An ultra-fast and efficient genomic tool for coverage calculation☆170Feb 9, 2026Updated 3 weeks ago
- haplotypic duplication identification tool☆275Oct 30, 2025Updated 4 months ago
- k-mer based assembly evaluation☆339Jun 28, 2024Updated last year
- ☆41May 19, 2025Updated 9 months ago
- Make colorful identity heatmaps of genomic sequence☆128May 24, 2024Updated last year
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆743Mar 18, 2025Updated 11 months ago
- Constructing a pangenome gene graph☆204Aug 11, 2025Updated 6 months ago
- 🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies☆122Feb 24, 2026Updated last week
- Identify and find telomeres, or telomeric repeats in a genome.☆158Nov 24, 2025Updated 3 months ago
- A collection of scripts for working with Hi-C data, Juicebox, and other genomic file formats☆69May 22, 2021Updated 4 years ago
- ☆29Feb 5, 2026Updated 3 weeks ago
- RepeatIdentifier☆71Mar 19, 2025Updated 11 months ago
- TEtrimmer: a novel tool to automate manual curation of transposable elements☆111Feb 24, 2026Updated last week
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆292Updated this week