Projects in Awesome Lists by OpenGene
A curated list of projects in awesome lists by OpenGene .
https://github.com/opengene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Last synced: 23 Jan 2026
https://github.com/OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Last synced: 07 May 2025
https://github.com/opengene/afterqc
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming
Last synced: 07 Mar 2026
https://github.com/OpenGene/AfterQC
Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming
Last synced: 05 May 2025
https://github.com/opengene/mutscan
Detect and visualize target mutations by scanning FastQ files directly
bioinformatics cancer detection fastq mutation ngs somatic validation variant visualization
Last synced: 10 Apr 2025
https://github.com/OpenGene/MutScan
Detect and visualize target mutations by scanning FastQ files directly
bioinformatics cancer detection fastq mutation ngs somatic validation variant visualization
Last synced: 09 May 2025
https://github.com/OpenGene/repaq
A fast lossless FASTQ compressor with ultra-high compression ratio
Last synced: 09 May 2025
https://github.com/opengene/repaq
A fast lossless FASTQ compressor with ultra-high compression ratio
Last synced: 05 Apr 2025
https://github.com/opengene/genefuse
Gene fusion detection and visualization
alk bioinformatics cancer cosmic eml4 fusion gene ret ros1
Last synced: 10 Apr 2025
https://github.com/opengene/gencore
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic
Last synced: 20 Aug 2025
https://github.com/OpenGene/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.
2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization
Last synced: 09 May 2025
https://github.com/opengene/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.
2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization
Last synced: 10 Apr 2025
https://github.com/opengene/fastplong
Ultra-fast preprocessing and quality control for long-read sequencing data
Last synced: 06 Apr 2025
https://github.com/OpenGene/GeneFuse
Gene fusion detection and visualization
alk bioinformatics cancer cosmic eml4 fusion gene ret ros1
Last synced: 09 May 2025
https://github.com/OpenGene/gencore
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic
Last synced: 09 May 2025
https://github.com/OpenGene/scrnapip
A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
Last synced: 09 May 2025
https://github.com/opengene/scrnapip
A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis
Last synced: 13 Feb 2026
https://github.com/opengene/opengene.jl
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Last synced: 10 Apr 2025
https://github.com/OpenGene/OpenGene.jl
(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia
Last synced: 22 Jul 2025
https://github.com/opengene/cfdnapattern
Pattern Recognition for Cell-free DNA
bioinformatics cfdna ngs pattern
Last synced: 20 Jul 2025
https://github.com/opengene/uniquekmer
Generate unique KMERs for every contig in a FASTA file
bioinformatics fasta kmer ngs sequencing unique virus
Last synced: 10 Apr 2025
https://github.com/opengene/ctdna-pipeline
A simplified pipeline for ctDNA sequencing data analysis
bioinformatics ctdna liquid-biopsy ngs pipeline
Last synced: 15 Oct 2025
https://github.com/opengene/visualmsi
Detect and visualize microsatellite instability(MSI) from NGS data
Last synced: 30 Aug 2025
https://github.com/opengene/defq
Please switch to https://github.com/OpenGene/defastq
demultiplexing demux dual-index fastq illumina index sequencing split
Last synced: 10 Apr 2025
https://github.com/opengene/mrbam
Query Mutated Reads from a Bam
accurate-frequency post-dedup unique-reads
Last synced: 10 Apr 2025
https://github.com/opengene/fusiondirect.jl
(No maintenance) Detect gene fusion directly from raw fastq files
bioinformatics cancer fusion gene ngs
Last synced: 12 Nov 2025
https://github.com/opengene/seqmaker.jl
(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated
bioinformatics illumina ngs simulation
Last synced: 12 Aug 2025
https://github.com/opengene/dedup
Deduplication for cfDNA sequencing data
bioinformatics ctdna deduplication liquid ngs
Last synced: 08 Jul 2025
https://github.com/opengene/defastq
Ultra-fast Multi-threaded FASTQ Demultiplexing
Last synced: 10 Apr 2025
https://github.com/opengene/pecheck
check paired-end FASTQ data integrity
bioinformatics check consistence fastq identical illumina integrity paired-end pe
Last synced: 30 Jun 2025
https://github.com/opengene/slicer
Slice a text file (like FastQ) to smaller files by lines, with gzip supported
file-cutter file-slicer file-splitter slicer splitter
Last synced: 15 Feb 2026
https://github.com/opengene/lungtcr
TCR Repertoire Analysis and Lung Cancer Prediction
Last synced: 16 Oct 2025
https://github.com/opengene/acmsi
The shiny-based app for Fragment Analysis, especially for MSI analysis
Last synced: 10 Apr 2025
https://github.com/opengene/irdproc
Process genomic data downloaded from influenza research database for unique k-mer generating
Last synced: 12 Nov 2025