Skip to content

@lbcb-sci Šikić lab

Change the repository type filter

All

    Repositories list

    23 repositories

    • 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
      •3•30•1•0•Updated Nov 22, 2024Nov 22, 2024

    • rockfish

      Public
      Python
      •
      MIT License
      •3•9•4•0•Updated Nov 18, 2024Nov 18, 2024

    • RiNALMo

      Public
      RiboNucleic Acid (RNA) Language Model
      bioinformaticsrna-seqbiologystructural-biologyrnalanguage-modelsecondary-structurerna-structure-predictionrna-secondary-structurefoundation-model
      Python
      •
      Apache License 2.0
      •10•73•1•0•Updated Nov 11, 2024Nov 11, 2024

    • 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 recommended).
      Rust
      •
      Other
      •11•197•33•6•Updated Nov 8, 2024Nov 8, 2024

    • I002C

      Public
      Telomere-to-Telomere diploid Indian Genome
      0•7•0•0•Updated May 9, 2024May 9, 2024

    • racon

      Public
      Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
      C++
      •
      MIT License
      •34•203•22•4•Updated Dec 29, 2023Dec 29, 2023

    • raven

      Public
      De novo genome assembler for long uncorrected reads
      C++
      •
      MIT License
      •21•205•27•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
      •21•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • T2T-assemblies

      Public
      T2T assemblies of human and durian genomes
      1•0•0•0•Updated May 4, 2023May 4, 2023

    • GNNs-Hamiltonian-cycles

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

    • MetagenomicsBenchmark

      Public
      Python
      •3•6•1•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://www.biorxiv.org/content/10.1101/720458v1
      C++
      •
      MIT License
      •45•67•22•1•Updated Aug 30, 2022Aug 30, 2022

    • hifiasm

      Public
      Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
      C++
      •
      MIT License
      •88•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•7•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•37•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