@OpenGene

OpenGene - Open Source Genetics Toolbox

Open source tools for NGS data analysis

Pinned repositories

  1. fastp

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

    C++ 364 77

  2. MutScan

    Detect and visualize target mutations by scanning FastQ files directly

    C 70 22

  3. CfdnaPattern

    Pattern Recognition for Cell-free DNA

    Python 32 17

  4. GeneFuse

    Gene fusion detection and visualization

    C 29 15

  5. gencore

    Generate consensus reads to reduce sequencing noises

    C++ 18 2

  6. repaq

    repack Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz (.rfq.xz)

    C 41 6

  • Gene fusion detection and visualization

    C 29 15 MIT Updated Sep 27, 2018
  • An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

    C++ 364 77 MIT Updated Sep 11, 2018
  • Generate consensus reads to reduce sequencing noises

    C++ 18 2 MIT Updated Sep 4, 2018
  • repack Illumina format FASTQ to a smaller binary file (.rfq), which can be further compressed by xz (.rfq.xz)

    C 41 6 MIT Updated Aug 17, 2018
  • Query Mutated Reads from a Bam

    Python 14 7 MIT Updated Aug 13, 2018
  • Pattern Recognition for Cell-free DNA

    Python 32 17 MIT Updated Aug 3, 2018
  • Detect and visualize target mutations by scanning FastQ files directly

    C 70 22 MIT Updated Aug 1, 2018
  • check paired-end FASTQ data integrity

    C 2 MIT Updated Aug 1, 2018
  • Ultra-fast Multi-threaded FASTQ Demultiplexing

    C 17 2 MIT Updated Jul 28, 2018
  • Classify somatic/germline mutations by deep neural networks

    Julia 6 3 Updated Mar 1, 2018
  • Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

    Python 121 41 MIT Updated Dec 29, 2017
  • awesome-bio-datasets

    48 14 MIT Updated Oct 28, 2017
  • Programming training for bioinformatics and other tasks, with introductions and tutorials.

    JavaScript 2 Updated Oct 27, 2017
  • Slice a text file (like FastQ) to smaller files by lines, with gzip supported

    C 3 1 MIT Updated Oct 18, 2017
  • OpenGene, core libraries for NGS data analysis and bioinformatics in julia

    Julia 53 13 Updated Oct 8, 2017
  • A simplified pipeline for ctDNA sequencing data analysis

    Shell 11 7 MIT Updated Sep 23, 2017
  • Detect gene fusion directly from raw fastq files

    Julia 21 10 Updated Aug 13, 2017
  • Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

    Julia 17 10 Updated Aug 10, 2017
  • Deduplication for cfDNA sequencing data

    Python 6 2 MIT Updated Jul 5, 2017
  • Liquid biopsy pocket book (in Chinese), written by HaploX engineers.

    CSS 11 8 Updated Jun 1, 2017
  • Quality control with BAM files

    Python 3 2 MIT Updated Apr 7, 2017