OpenGene - Open Source Genetics Toolbox

Repositories

• fastv

  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.

  visualization bioinformatics virus ngs sequencing viral 2019-ncov
  C++ MIT 5 32 3 0 Updated Jun 1, 2020

• UniqueKMER

  Generate unique KMERs for every contig in a FASTA file

  bioinformatics virus ngs sequencing fasta kmer unique
  C MIT 0 3 0 0 Updated May 25, 2020

• GeneFuse

  Gene fusion detection and visualization

  bioinformatics gene cancer fusion cosmic alk eml4
  C MIT 35 57 19 0 Updated May 21, 2020

• AfterQC

  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

  bioinformatics quality-control ngs sequencing overlap error trimming
  Python MIT 51 156 22 1 Updated May 14, 2020

• fastp

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

  adapter quality bioinformatics quality-control filter ngs sequencing
  C++ MIT 159 761 108 3 Updated Apr 8, 2020

• gencore

  Generate consensus reads to reduce sequencing noises and remove duplications

  bioinformatics ngs sequencing consensus duplication deep-sequencing sequencing-error
  C++ MIT 18 65 15 0 Updated Mar 18, 2020

• repaq

  A fast lossless FASTQ compressor with ultra-high compression ratio
  C MIT 13 69 6 0 Updated Mar 16, 2020

• MutScan

  Detect and visualize target mutations by scanning FastQ files directly

  visualization bioinformatics validation cancer detection ngs mutation
  C MIT 33 104 2 0 Updated Jan 21, 2020

• VisualMSI

  Detect and visualize microsatellite instability(MSI) from NGS data
  C++ MIT 6 20 3 0 Updated Jun 4, 2019

• novelbio-base
  Java 0 2 0 0 Updated Mar 6, 2019

• novelbio-bioinfo
  Java 0 2 0 0 Updated Mar 3, 2019

• MrBam

  Query Mutated Reads from a Bam

  unique-reads post-dedup accurate-frequency
  Python MIT 10 18 2 0 Updated Nov 26, 2018

• CfdnaPattern

  Pattern Recognition for Cell-free DNA

  bioinformatics pattern ngs cfdna
  Python MIT 20 44 3 1 Updated Aug 3, 2018

• pecheck

  check paired-end FASTQ data integrity

  bioinformatics check integrity pe consistence illumina fastq
  C MIT 1 3 1 0 Updated Jul 31, 2018

• defq

  Ultra-fast Multi-threaded FASTQ Demultiplexing

  split sequencing index illumina fastq demultiplexing demux
  C MIT 4 22 1 0 Updated Jul 27, 2018

• awesome-bio-datasets

  awesome-bio-datasets
  MIT 29 106 0 0 Updated Oct 28, 2017

• slicer

  Slice a text file (like FastQ) to smaller files by lines, with gzip supported

  splitter slicer file-splitter file-cutter file-slicer
  C MIT 3 5 0 0 Updated Oct 18, 2017

• OpenGene.jl

  (No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

  bioinformatics julia ngs
  Julia 14 59 8 0 Updated Oct 8, 2017

• ctdna-pipeline

  A simplified pipeline for ctDNA sequencing data analysis

  bioinformatics pipeline ngs ctdna liquid-biopsy
  Shell MIT 12 24 2 0 Updated Sep 23, 2017

• FusionDirect.jl

  (No maintenance) Detect gene fusion directly from raw fastq files

  bioinformatics gene cancer ngs fusion
  Julia 14 23 5 1 Updated Aug 12, 2017

• SeqMaker.jl

  (No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

  bioinformatics simulation ngs illumina
  Julia 10 19 6 0 Updated Aug 10, 2017

• dedup

  Deduplication for cfDNA sequencing data

  bioinformatics ngs liquid deduplication ctdna
  Python MIT 5 8 2 0 Updated Jul 5, 2017