OpenGene - Open Source Genomics Toolbox

All

27 repositories

fastp
Public
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter quality quality-control sequencing overlap splitting duplication umi trimming preprocessing
C++
•
MIT License
•334•1.9k•341•14•Updated Nov 8, 2024Nov 8, 2024
fastplong
Public
Ultra-fast preprocessing and quality control for long-read sequencing data
C++
•
MIT License
•3•48•0•0•Updated Nov 7, 2024Nov 7, 2024
repaq
Public
A fast lossless FASTQ compressor with ultra-high compression ratio
C
•
MIT License
•19•124•8•0•Updated Oct 22, 2024Oct 22, 2024
ACMSI
Public
The shiny-based app for Fragment Analysis, especially for MSI analysis
R
•0•4•0•0•Updated Jun 28, 2024Jun 28, 2024
gencore
Public
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
duplex consensus duplication deduplication somatic deep-sequencing sequencing-error sequencing-noise duplex-sequencing bioinformatics
C++
•
MIT License
•32•115•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•111•14•0•Updated Oct 27, 2023Oct 27, 2023
scrnapip
Public
A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
HTML
•15•103•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
•8•43•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 ngs julia
Julia
•
Other
•15•64•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
•
MIT License
•63•115•33•0•Updated Feb 21, 2022Feb 21, 2022
MutScan
Public
Detect and visualize target mutations by scanning FastQ files directly
visualization bioinformatics validation detection ngs mutation variant fastq somatic cancer
C
•
MIT License
•38•149•6•0•Updated Feb 10, 2022Feb 10, 2022
defastq
Public
Ultra-fast Multi-threaded FASTQ Demultiplexing
C++
•
MIT License
•1•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 ngs sequencing overlap error trimming filtering fastq qc adapter-trimming
Python
•
MIT License
•51•207•25•1•Updated May 14, 2020May 14, 2020
VisualMSI
Public
Detect and visualize microsatellite instability(MSI) from NGS data
C++
•
MIT License
•11•31•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
•20•57•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
•6•29•2•0•Updated Jul 28, 2018Jul 28, 2018
awesome-bio-datasets
Public
awesome-bio-datasets
MIT License
•42•218•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
•
MIT License
•16•36•2•0•Updated Sep 23, 2017Sep 23, 2017
FusionDirect.jl
Public
(No maintenance) Detect gene fusion directly from raw fastq files
bioinformatics cancer ngs gene fusion
Julia
•
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
•10•24•6•0•Updated Aug 10, 2017Aug 10, 2017
dedup
Public
Deduplication for cfDNA sequencing data
bioinformatics ngs liquid deduplication ctdna
Python
•
MIT License
•4•10•2•0•Updated Jul 5, 2017Jul 5, 2017