A PyTorch Basecaller for Oxford Nanopore Reads
☆436Feb 20, 2026Updated 7 months ago
Alternatives and similar repositories for bonito
Users that are interested in bonito are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by a…☆205May 4, 2023Updated 3 years ago
- Methylation/modified base calling separated from basecalling.☆189Sep 17, 2024Updated 2 years ago
- Neural-network consensus polishing and variant calling for Oxford Nanopore sequencing data☆527May 20, 2026Updated 4 months ago
- Training models for basecalling Oxford Nanopore reads☆116Jan 13, 2022Updated 4 years ago
- Flip-flop basecaller for Oxford Nanopore reads☆97Jan 13, 2022Updated 4 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Oxford Nanopore's Basecaller☆875Sep 3, 2026Updated 2 weeks ago
- Nanopore basecalling and consensus decoding☆46Jul 22, 2022Updated 4 years ago
- Signal-level algorithms for MinION data☆603Aug 5, 2023Updated 3 years ago
- PEPPER-Margin-DeepVariant☆261Jan 12, 2024Updated 2 years ago
- Oxford Nanopore Technologies fast5 API software☆155Feb 27, 2024Updated 2 years ago
- Read Until client library for Nanopore Sequencing☆108Sep 25, 2024Updated last year
- SquiggleKit: A toolkit for manipulating nanopore signal data☆130Feb 16, 2024Updated 2 years ago
- Research release basecalling models and configurations☆121Sep 7, 2026Updated last week
- A comparison of different Oxford Nanopore basecallers☆316Aug 5, 2019Updated 7 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆27Dec 29, 2020Updated 5 years ago
- CLI tool for flexible and fast adaptive sampling on ONT sequencers☆198Feb 25, 2026Updated 6 months ago
- De novo assembler for single molecule sequencing reads using repeat graphs☆950Apr 3, 2026Updated 5 months ago
- Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)☆166Aug 21, 2026Updated 3 weeks ago
- [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads☆272Oct 13, 2022Updated 3 years ago
- ☆16Apr 8, 2020Updated 6 years ago
- A basecaller for Oxford Nanopore Technologies' sequencers☆121Jul 6, 2023Updated 3 years ago
- Pod5: a high performance file format for nanopore reads.☆177Aug 24, 2026Updated 3 weeks ago
- Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.☆232May 4, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Long read aligner☆115May 26, 2023Updated 3 years ago
- Slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format.☆106Aug 26, 2026Updated 3 weeks ago
- Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling☆392Updated this week
- Very fast ONT basecaller☆52Jun 17, 2022Updated 4 years ago
- A short analysis of Oxford Nanopore consensus accuracy for bacterial genome assemblies☆60Aug 6, 2019Updated 7 years ago
- Data and analysis for NA12878 genome on nanopore☆413Nov 22, 2022Updated 3 years ago
- Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)☆118Mar 2, 2026Updated 6 months ago
- Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…☆303May 9, 2024Updated 2 years ago
- Nanopore sequence read simulator☆311Mar 12, 2026Updated 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.
- High-quality Nanopore-only genome polisher☆71Aug 16, 2024Updated 2 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,249May 19, 2026Updated 4 months ago
- Plotting scripts for long read sequencing data☆560Sep 5, 2026Updated 2 weeks ago
- DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications☆104Mar 8, 2023Updated 3 years ago
- pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…☆284Oct 18, 2024Updated last year
- Long read / genome alignment software☆331Dec 16, 2025Updated 9 months ago
- Structural variation caller using third generation sequencing☆679Sep 10, 2026Updated last week