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@OpenGene

OpenGene - Open Source Genomics Toolbox

Open source tools for NGS data analysis

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  1. fastp Public

    An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

    C++ 2.1k 345

  2. MutScan Public

    Detect and visualize target mutations by scanning FastQ files directly

    C 153 38

  3. GeneFuse Public

    Gene fusion detection and visualization

    C 128 59

  4. gencore Public

    Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

    C++ 121 31

  5. repaq Public

    A fast lossless FASTQ compressor with ultra-high compression ratio

    C 139 20

  6. fastplong Public

    Ultra-fast preprocessing and quality control for long-read sequencing data

    C++ 156 7

Repositories

Showing 10 of 30 repositories
  • parallel Public

    Python scripts to process files within a folder in parallel, with tools like fastp

    Python 1 MIT 0 0 0 Updated Jul 3, 2025
  • fastp Public

    An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

    C++ 2,114 MIT 344 354 17 Updated Jul 2, 2025
  • fastplong Public

    Ultra-fast preprocessing and quality control for long-read sequencing data

    C++ 156 MIT 7 11 0 Updated May 30, 2025
  • repaq Public

    A fast lossless FASTQ compressor with ultra-high compression ratio

    C 139 MIT 20 9 0 Updated May 28, 2025
  • ECCFP Public Forked from WSG-Lab/ECCFP
    Python 0 MIT 2 0 0 Updated May 21, 2025
  • LungTCR Public

    TCR Repertoire Analysis and Lung Cancer Prediction

    R 4 MIT 2 0 0 Updated Apr 21, 2025
  • ACMSI Public

    The shiny-based app for Fragment Analysis, especially for MSI analysis

    R 7 0 0 0 Updated Jun 28, 2024
  • gencore Public

    Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

    C++ 121 MIT 31 41 0 Updated Oct 27, 2023
  • fastv Public

    An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

    C++ 118 MIT 24 14 0 Updated Oct 27, 2023
  • scrnapip Public

    A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis

    HTML 109 15 5 0 Updated Oct 16, 2023

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