PBSIM3: a simulator for all types of PacBio and ONT long reads
☆120Apr 22, 2025Updated last year
Alternatives and similar repositories for pbsim3
Users that are interested in pbsim3 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- implicit pangenome graph☆114Updated this week
- Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads☆88May 27, 2026Updated 4 months ago
- Enumerating bubbles in pangenome graphs☆16Oct 9, 2026Updated last week
- Multiple sequence alignment of long tandem repeats☆34Oct 9, 2026Updated last week
- ☆45Dec 29, 2025Updated 9 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.
- Sequence-to-graph mapper and graph generator☆492Aug 11, 2025Updated last year
- a long read simulator that can imitate many types of read problems☆308Jul 24, 2026Updated 2 months ago
- Efficient low-divergence mapping of long reads in minimizer space☆70Oct 7, 2023Updated 3 years ago
- PBSIM2: a simulator for long read sequencers with a novel generative model of quality scores☆76Jul 22, 2023Updated 3 years ago
- A complete diploid human genome☆161Aug 10, 2026Updated 2 months ago
- ☆291Dec 29, 2025Updated 9 months ago
- k-mer based assembly evaluation☆354Jul 6, 2026Updated 3 months ago
- Long read / genome alignment software☆332Dec 16, 2025Updated 10 months ago
- ☆63Sep 15, 2025Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Hifiasm: a haplotype-resolved assembler for accurate Hifi reads☆817May 31, 2026Updated 4 months ago
- Graphical interactive tool for the visualization of sequence graphs in GFA format.☆76Feb 19, 2019Updated 7 years ago
- recompute GFA link overlaps☆26Sep 14, 2022Updated 4 years ago
- Programs implementing the trio-binning genome assembly method☆22Nov 22, 2023Updated 2 years ago
- An accurate aligner of long reads to a variation graph, based on co-linear chaining☆35May 23, 2025Updated last year
- Transformer-based sequence correction method for genome assembly polishing☆111Mar 11, 2025Updated last year
- Long-read aligner to pangenome graphs☆29May 20, 2024Updated 2 years ago
- abPOA: an SIMD-based C library for fast partial order alignment using adaptive band☆148Sep 17, 2026Updated last month
- Successor of bwa-mem for short-read alignment☆352Oct 1, 2026Updated 2 weeks 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.
- Peregrine: Fast Genome Assembler Using SHIMMER Index☆102Feb 6, 2022Updated 4 years ago
- bioinformatics toolkit in rust☆109Aug 16, 2026Updated 2 months ago
- SRF: Satellite Repeat Finder☆110Jan 8, 2024Updated 2 years ago
- Genome browser 🧬👀🚀☆35Aug 24, 2026Updated last month
- A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.☆52Dec 9, 2025Updated 10 months ago
- Shared k-mer content between two genomes☆19Jun 21, 2023Updated 3 years ago
- RepeatIdentifier☆75Mar 19, 2025Updated last year
- Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…☆421Aug 25, 2026Updated last month
- Fast and exact gap-affine partial order alignment☆71Sep 16, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Extracting paths from assembly graphs☆26Jun 22, 2026Updated 3 months ago
- LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads☆111Jun 25, 2026Updated 3 months ago
- base-accurate DNA sequence alignments using WFA and mashmap3☆225Sep 28, 2026Updated 2 weeks ago
- Mumemto: multi-MUM and MEM finding across pangenomes☆139Sep 21, 2026Updated 3 weeks ago
- alignment to variation graph inducer☆165Jul 29, 2026Updated 2 months ago
- convert variation graph alignments to coverage maps over nodes☆28Jan 21, 2026Updated 8 months ago
- Hybrid error correction approach for long reads using overlap graph☆11Sep 26, 2023Updated 3 years ago