OpenGene - Open Source Genomics Toolbox

All

30 repositories

fastp
Public
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter quality bioinformatics quality-control filter ngs sequencing overlap splitting duplication
C++
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MIT License
•355•2.2k•361•18•Updated Oct 14, 2025Oct 14, 2025
fastplong
Public
Ultra-fast preprocessing and quality control for long-read sequencing data
C++
•
MIT License
•9•194•13•0•Updated Sep 6, 2025Sep 6, 2025
LungTCR
Public
TCR Repertoire Analysis and Lung Cancer Prediction
R
•
MIT License
•2•5•0•0•Updated Aug 6, 2025Aug 6, 2025
parallel
Public
Python scripts to process files within a folder in parallel, with tools like fastp
Python
•
MIT License
•0•1•0•0•Updated Jul 6, 2025Jul 6, 2025
repaq
Public
A fast lossless FASTQ compressor with ultra-high compression ratio
C
•
MIT License
•20•142•9•0•Updated May 28, 2025May 28, 2025
ECCFP
Public
Python
•
MIT License
•2•0•0•0•Updated May 21, 2025May 21, 2025
ACMSI
Public
The shiny-based app for Fragment Analysis, especially for MSI analysis
R
•0•7•0•0•Updated Jun 28, 2024Jun 28, 2024
gencore
Public
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
bioinformatics duplex ngs sequencing consensus duplication deduplication somatic deep-sequencing sequencing-error
C++
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MIT License
•31•125•41•0•Updated Oct 27, 2023Oct 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.
visualization bioinformatics virus ngs sequencing viral 2019-ncov coronavirus covid-19 covid
C++
•
MIT License
•24•117•14•0•Updated Oct 27, 2023Oct 27, 2023
scrnapip
Public
A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
HTML
•16•112•5•0•Updated Oct 16, 2023Oct 16, 2023
UniqueKMER
Public
Generate unique KMERs for every contig in a FASTA file
bioinformatics virus ngs sequencing fasta kmer unique
C
•
MIT License
•7•48•5•0•Updated Aug 17, 2022Aug 17, 2022
OpenGene.jl
Public
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
bioinformatics julia ngs
Julia
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Other
•15•66•8•0•Updated Jul 18, 2022Jul 18, 2022
GeneFuse
Public
Gene fusion detection and visualization
bioinformatics gene cancer fusion cosmic alk eml4 ros1 ret
C
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MIT License
•59•128•34•1•Updated Feb 21, 2022Feb 21, 2022
MutScan
Public
Detect and visualize target mutations by scanning FastQ files directly
visualization bioinformatics validation cancer detection ngs mutation variant fastq somatic
C
•
MIT License
•37•154•6•0•Updated Feb 10, 2022Feb 10, 2022
defastq
Public
Ultra-fast Multi-threaded FASTQ Demultiplexing
C++
•
MIT License
•2•8•2•0•Updated Sep 28, 2021Sep 28, 2021
IRDProc
Public
Process genomic data downloaded from influenza research database for unique k-mer generating
Python
•
MIT License
•0•1•0•0•Updated Jul 30, 2020Jul 30, 2020
AfterQC
Public
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
bioinformatics quality-control ngs sequencing overlap error trimming filtering fastq qc
Python
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MIT License
•53•212•26•2•Updated May 14, 2020May 14, 2020
VisualMSI
Public
Detect and visualize microsatellite instability(MSI) from NGS data
C++
•
MIT License
•10•32•3•0•Updated Jun 4, 2019Jun 4, 2019
novelbio-base
Public
Java
•0•2•0•0•Updated Mar 6, 2019Mar 6, 2019
novelbio-bioinfo
Public
Java
•0•2•0•0•Updated Mar 3, 2019Mar 3, 2019
MrBam
Public
Query Mutated Reads from a Bam
unique-reads post-dedup accurate-frequency
Python
•
MIT License
•7•26•3•0•Updated Nov 26, 2018Nov 26, 2018
CfdnaPattern
Public
Pattern Recognition for Cell-free DNA
bioinformatics pattern ngs cfdna
Python
•
MIT License
•21•59•3•1•Updated Aug 3, 2018Aug 3, 2018
pecheck
Public
check paired-end FASTQ data integrity
bioinformatics check integrity pe consistence illumina fastq paired-end identical
C
•
MIT License
•3•6•1•0•Updated Aug 1, 2018Aug 1, 2018
defq
Public
Please switch to https://github.com/OpenGene/defastq
split sequencing index illumina fastq demultiplexing demux dual-index
C
•
MIT License
•7•29•2•0•Updated Jul 28, 2018Jul 28, 2018
awesome-bio-datasets
Public
awesome-bio-datasets
MIT License
•47•239•0•0•Updated Oct 28, 2017Oct 28, 2017
slicer
Public
Slice a text file (like FastQ) to smaller files by lines, with gzip supported
splitter slicer file-splitter file-cutter file-slicer
C
•
MIT License
•2•6•0•0•Updated Oct 18, 2017Oct 18, 2017
ctdna-pipeline
Public
A simplified pipeline for ctDNA sequencing data analysis
bioinformatics pipeline ngs ctdna liquid-biopsy
Shell
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MIT License
•16•37•2•0•Updated Sep 23, 2017Sep 23, 2017
FusionDirect.jl
Public
(No maintenance) Detect gene fusion directly from raw fastq files
bioinformatics gene cancer ngs fusion
Julia
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Other
•16•25•5•1•Updated Aug 13, 2017Aug 13, 2017
SeqMaker.jl
Public
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
bioinformatics simulation ngs illumina
Julia
•
Other
•8•24•6•0•Updated Aug 10, 2017Aug 10, 2017
dedup
Public
Deduplication for cfDNA sequencing data
bioinformatics ngs liquid deduplication ctdna
Python
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MIT License
•4•11•2•0•Updated Jul 5, 2017Jul 5, 2017