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Šikić lab

A computational group with a focus on the development of new algorithms and AI models for the analysis of DNA and RNA sequencing data and biomolecular strucures

Popular repositories Loading

  1. racon racon Public

    Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

    C++ 217 34

  2. raven raven Public

    De novo genome assembler for long uncorrected reads

    C++ 214 20

  3. herro 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 207 13

  4. RiNALMo RiNALMo Public

    RiboNucleic Acid (RNA) Language Model

    Python 92 17

  5. graphmap2 graphmap2 Public

    Forked from isovic/graphmap

    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/10.1101/7204…

    C++ 67 6

  6. ra ra Public

    Forked from rvaser/ra

    Assembler for raw de novo genome assembly of long uncorrected reads.

    Python 37 4

Repositories

Showing 10 of 25 repositories
  • I002C Public

    Telomere-to-Telomere diploid Indian Genome

    7 0 0 0 Updated Mar 28, 2025
  • metaxa Public
    Python 0 GPL-3.0 0 0 0 Updated Mar 25, 2025
  • RiNALMo Public

    RiboNucleic Acid (RNA) Language Model

    Python 92 Apache-2.0 17 2 0 Updated Mar 24, 2025
  • BadRead-Meta-Fork Public

    BeadRead fork for metagenomics classification

    Python 0 GPL-3.0 0 0 0 Updated Mar 20, 2025
  • GNNome Public

    A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.

    Python 34 BSD-3-Clause 4 1 0 Updated Mar 11, 2025
  • 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 207 13 39 7 Updated Feb 7, 2025
  • rockfish Public
    Python 10 MIT 3 5 0 Updated Nov 18, 2024
  • racon Public

    Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

    C++ 217 MIT 34 23 4 Updated Dec 29, 2023
  • raven Public

    De novo genome assembler for long uncorrected reads

    C++ 214 MIT 20 27 2 Updated Nov 15, 2023
  • roko Public

    A deep learning consensus polisher

    Python 7 GPL-3.0 2 0 3 Updated Oct 3, 2023
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