Inference of ploidy and heterozygosity structure using whole genome sequencing data
☆294Feb 25, 2026Updated 2 months ago
Alternatives and similar repositories for smudgeplot
Users that are interested in smudgeplot are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reference-free profiling of polyploid genomes☆145Oct 2, 2025Updated 7 months ago
- Fast genome analysis from unassembled short reads☆320Apr 8, 2024Updated 2 years ago
- A genome completeness evaluation tool based on miniprot☆242Sep 18, 2025Updated 8 months ago
- k-mer based assembly evaluation☆343Jun 28, 2024Updated last year
- haplotypic duplication identification tool☆285Oct 30, 2025Updated 6 months 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.
- Fast and frugal disk based k-mer counter☆14Apr 1, 2021Updated 5 years ago
- A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification☆171Oct 29, 2025Updated 6 months ago
- A gap-closing software tool that uses long reads to enhance genome assembly.☆239Sep 6, 2024Updated last year
- Tools for fast and flexible genome assembly scaffolding and improvement☆563Feb 14, 2024Updated 2 years ago
- Find, circularise and annotate mitogenome from PacBio assemblies☆196May 11, 2025Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆391Apr 22, 2026Updated 3 weeks ago
- Synteny and Rearrangement Identifier☆467Mar 17, 2026Updated 2 months ago
- HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data☆268Jan 5, 2026Updated 4 months ago
- Extensive de-novo TE Annotator☆446May 12, 2026Updated last week
- 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.
- Yet another Hi-C scaffolding tool☆180Nov 4, 2024Updated last year
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆214May 10, 2026Updated last week
- Identify and find telomeres, or telomeric repeats in a genome.☆164Nov 24, 2025Updated 5 months ago
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- Fast and frugal disk based k-mer counter☆332May 8, 2026Updated last week
- Tool to plot synteny and structural rearrangements between genomes☆346Apr 7, 2025Updated last year
- A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.☆210Nov 18, 2022Updated 3 years ago
- Generate an interactive dot plot from mummer or minimap alignments☆217Jan 17, 2024Updated 2 years ago
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆772Apr 15, 2026Updated last month
- 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.
- To phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.☆70Mar 23, 2025Updated last year
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆189May 17, 2024Updated 2 years ago
- Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.☆177Apr 22, 2026Updated 3 weeks ago
- Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)☆380Feb 13, 2025Updated last year
- Fast and accurately polish the genome generated by long reads.☆243Jan 9, 2025Updated last year
- Align proteins to genomes with splicing and frameshift☆402Jan 5, 2026Updated 4 months ago
- software tools for haplotype assembly from sequence data☆231Feb 9, 2025Updated last year
- the pangenome graph builder☆495Mar 31, 2026Updated last month
- WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes☆164Nov 4, 2025Updated 6 months ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the sc…☆149Apr 13, 2026Updated last month
- ☆241Jan 24, 2025Updated last year
- SRF: Satellite Repeat Finder☆102Jan 8, 2024Updated 2 years ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆216Mar 20, 2026Updated 2 months ago
- Fast and accurate de novo assembler for long reads☆402May 10, 2024Updated 2 years ago
- An accurate GFF3/GTF lift over pipeline☆537Aug 1, 2023Updated 2 years ago
- Yet another k-mer analyzer☆171Dec 30, 2025Updated 4 months ago