Tools for fast and flexible genome assembly scaffolding and improvement
☆578Oct 1, 2026Updated 3 weeks ago
Alternatives and similar repositories for RagTag
Users that are interested in RagTag are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- k-mer based assembly evaluation☆357Jul 6, 2026Updated 3 months ago
- An accurate GFF3/GTF lift over pipeline☆562Aug 1, 2023Updated 3 years ago
- Synteny and Rearrangement Identifier☆496Jul 1, 2026Updated 3 months ago
- haplotypic duplication identification tool☆298Oct 30, 2025Updated 11 months ago
- RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag☆173May 30, 2021Updated 5 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.
- Tool to plot synteny and structural rearrangements between genomes☆359Jul 27, 2026Updated 3 months 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…☆469Jun 17, 2026Updated 4 months ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆818May 31, 2026Updated 4 months ago
- A genome completeness evaluation tool based on miniprot☆270Oct 7, 2026Updated 3 weeks ago
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆422Updated this week
- A gap-closing software tool that uses long reads to enhance genome assembly.☆251Sep 6, 2024Updated 2 years ago
- Fast and accurate de novo assembler for long reads☆407May 10, 2024Updated 2 years ago
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆213Nov 18, 2022Updated 3 years ago
- Fast and accurately polish the genome generated by long reads.☆247Jan 9, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Yet another Hi-C scaffolding tool☆185Nov 4, 2024Updated last year
- ☆278Jun 26, 2025Updated last year
- Inference of ploidy and heterozygosity structure using whole genome sequencing data☆305Sep 23, 2026Updated last month
- Official home of genome aligner based upon notion of Cactus graphs☆716Updated this week
- Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/☆588Sep 7, 2026Updated last month
- the pangenome graph builder☆522Jul 24, 2026Updated 3 months ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆204May 11, 2025Updated last year
- Long read / genome alignment software☆333Dec 16, 2025Updated 10 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Chromosome-level scaffolding using multiple references☆170Sep 8, 2024Updated 2 years ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆191Jun 23, 2026Updated 4 months ago
- Extensive de-novo TE Annotator☆472Sep 10, 2026Updated last month
- De-Novo Repeat Discovery Tool☆248Updated this week
- Mummer alignment tool☆578Feb 4, 2025Updated last year
- A program for assessing the T2T genome continuity and completeness☆98Oct 13, 2026Updated 2 weeks ago
- Align proteins to genomes with splicing and frameshift☆425Jan 5, 2026Updated 9 months ago
- A single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulatio…☆131Jun 18, 2026Updated 4 months ago
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆220Jun 30, 2026Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Python library to facilitate genome assembly, annotation, and comparative genomics☆933Sep 19, 2026Updated last month
- A genomic k-mer counter (and sequence utility) with nice features.☆193Jul 21, 2026Updated 3 months ago
- Long read based human genomic structural variation detection with cuteSV☆296Oct 12, 2026Updated 2 weeks ago
- Identify and find telomeres, or telomeric repeats in a genome.☆180Updated this week
- Evaluation and polishing workflows for T2T genome assemblies☆175Sep 15, 2026Updated last month
- De novo assembler for single molecule sequencing reads using repeat graphs☆954Apr 3, 2026Updated 6 months ago
- Sequence-to-graph mapper and graph generator☆492Aug 11, 2025Updated last year