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    30 repositories

    • GFMs

      Public
      Source code for the paper "Entropy, Disagreement, and the Limits of Foundation Models in Genomics"
      Python
      •0•2•0•0•Updated Apr 15, 2026Apr 15, 2026

    • herro

      Public
      HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommend…
      Rust
      •
      Other
      •16•242•40•6•Updated Apr 13, 2026Apr 13, 2026

    • T2T-assemblies

      Public
      T2T assemblies of human and durian genomes
      1•0•0•0•Updated Apr 2, 2026Apr 2, 2026

    • StrainRefine

      Public
      Post-mapping refinement method for strain-level metagenomic classification that analyzes read–reference mapping profiles to reduce false positives.
      Python
      •0•1•0•0•Updated Mar 12, 2026Mar 12, 2026

    • I002C

      Public
      Telomere-to-Telomere diploid Indian Genome
      0•9•0•0•Updated Feb 9, 2026Feb 9, 2026

    • Campolina

      Public
      Python
      •
      MIT License
      •1•10•1•0•Updated Dec 24, 2025Dec 24, 2025

    • GNNome

      Public
      A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •8•52•2•0•Updated Dec 9, 2025Dec 9, 2025

    • MADRe

      Public
      Strain-level metagenomic classification with Metagenome Assembly driven Database Reduction approach
      Python
      •
      MIT License
      •3•11•0•1•Updated Nov 6, 2025Nov 6, 2025

    • RiNALMo

      Public
      RiboNucleic Acid (RNA) Language Model
      bioinformaticsrna-seqbiology
      bioinformaticsrna-seqbiologystructural-biologyrnalanguage-modelsecondary-structurerna-structure-predictionrna-secondary-structurefoundation-model
      Python
      •
      Apache License 2.0
      •38•161•1•0•Updated Oct 3, 2025Oct 3, 2025

    • DipGNNome

      Public
      Python
      •0•1•0•0•Updated Sep 15, 2025Sep 15, 2025

    • metaxa

      Public
      Python
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Mar 25, 2025Mar 25, 2025

    • BadRead-Meta-Fork

      Public
      BeadRead fork for metagenomics classification
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 20, 2025Mar 20, 2025

    • rockfish

      Public
      Python
      •
      MIT License
      •3•12•5•0•Updated Nov 18, 2024Nov 18, 2024

    • racon

      Public
      Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
      C++
      •
      MIT License
      •33•239•23•4•Updated Dec 29, 2023Dec 29, 2023

    • raven

      Public
      De novo genome assembler for long uncorrected reads
      C++
      •
      MIT License
      •19•231•28•2•Updated Nov 15, 2023Nov 15, 2023

    • roko

      Public
      A deep learning consensus polisher
      Python
      •
      GNU General Public License v3.0
      •2•7•0•3•Updated Oct 3, 2023Oct 3, 2023

    • heron-raven

      Public
      Development of Raven - Heron branch
      C++
      •
      MIT License
      •19•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • GNNs-Hamiltonian-cycles

      Public
      Supplementary code for "Finding Hamiltonian cycles with graph neural networks"
      Python
      •
      MIT License
      •3•5•0•0•Updated May 2, 2023May 2, 2023

    • MetagenomicsBenchmark

      Public
      Python
      •4•7•2•0•Updated Oct 26, 2022Oct 26, 2022

    • ram

      Public
      C++
      •
      MIT License
      •4•5•1•0•Updated Oct 19, 2022Oct 19, 2022

    • graphmap2

      Public
      GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https:/…
      C++
      •
      MIT License
      •43•70•23•0•Updated Aug 30, 2022Aug 30, 2022

    • hifiasm

      Public
      Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
      C++
      •
      MIT License
      •112•0•0•0•Updated Jul 13, 2022Jul 13, 2022

    • ratlesnake

      Public
      C++
      •
      MIT License
      •1•3•0•0•Updated Oct 24, 2021Oct 24, 2021

    • merlion

      Public
      C++
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2021Oct 7, 2021

    • Rockfish-old

      Public archive
      Deep learning based method for detecting DNA base modifications
      Python
      •
      GNU General Public License v3.0
      •1•2•0•1•Updated Jun 11, 2021Jun 11, 2021

    • tarantula

      Public
      C++
      •
      MIT License
      •0•0•0•0•Updated Jun 4, 2021Jun 4, 2021

    • NeuralLayout

      Public
      A GNN model that executes simplification algorithms used in the layout phase of de novo genome assembly process.
      Python
      •
      MIT License
      •3•0•0•0•Updated May 24, 2021May 24, 2021

    • ScaRa

      Public
      SCARA - scaffolding with long reads
      C++
      •
      MIT License
      •2•8•0•0•Updated Feb 17, 2021Feb 17, 2021

    • ra

      Public
      Assembler for raw de novo genome assembly of long uncorrected reads.
      Python
      •
      MIT License
      •9•35•7•0•Updated Dec 11, 2019Dec 11, 2019

    • RNAseqEval

      Public
      A tool for evaluating RNA seq mapping
      Python
      •11•0•0•0•Updated Oct 25, 2019Oct 25, 2019
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