Luo Lab

Software

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Gungnir
Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power
[bioRxiv]
2025
Governome
A new standard in genomic data privacy that realizes owner-governance
[Cell Reports Methods]
2025
Clair3-RNA
ONT small variant caller for RNA sequencing data
[bioRxiv]
2025
Repun
Accurate small variant representation unification method for multiple sequencing platforms
[Briefings in Bioinformatics]
2025
AutoPM3
Enhancing variant interpretation via LLM-driven PM3 evidence extraction
[Bioinformatics]
2025
CellContrast
Reconstructing spatial relationships in scRNA-seq data via deep contrastive learning
[Patterns]
2024
ClairS-TO
ONT somatic variant caller for tumor-only samples
[bioRxiv]
2024
ClairS
ONT somatic variant caller for paired tumor-normal samples
[bioRxiv]
2023
ClusterV
Find HIV quasispecies and drug resistance using ONT sequencing
[Clin. Chem]
2023
ONT-TB-NF
Nextflow pipeline for TB antibiotic-resistance detection from ONT adaptive sequencing
[Scientific Reports]
2023
Duet
SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing
[BMC Bioinformatics]
2022
Clair3-Trio
ONT family trio variant caller
[Briefings in Bioinformatics]
2022
Clair3
ONT small variant caller Gen3 - Symphonizing pileup and full-alignment
[Nat. Comp. Sci.]
2022
SENSV
Detecting structural variations with precise breakpoints using low-depth WGS
[Sci. Rep.]
2022
ECNano
Cost-effective workflow for target enrichment sequencing on 4800 genes
[BMC Medical Genomics]
2022
HKG
Variant database with 205 Hong Kong Cantonese exomes
[NAR Genomics]
2022
RENET2
Full-text Gene-Disease Relation Extraction with iterative training
[NAR Genomics]
2021
CONNET
Improving ONT data genome assembly consensus quality
[iScience]
2020
Clair
ONT small variant caller Gen2
[Nat. Mach. Intell.]
2020
RENET
Deep learning approach for extracting gene-disease associations
[RECOMB 2019]
2019
Clairvoyante
ONT small variant caller Gen1 - Multi-task CNN
[Nat. Comm.]
2019
16GT
Small variant caller using a 16-genotype probabilistic model
[GigaScience]
2017
LRSim
Linked-Reads Simulator
[Comp. Struct. Biotech. J.]
2017
BASE
Assembly method for large genomes using longer NGS reads
[BMC Genomics]
2016
MICA
Fast short-read aligner using Intel MIC Architecture
[BMC Bioinformtics]
2015
MEGAHIT
Ultra-fast metagenomics assembler using succinct de Bruijn graph
[Bioinformatics]
2015
database.bio
Web application for interpreting human variations
[Bioinformatics]
2015
BALSA
Integrated secondary analysis for whole-genome and whole-exome sequencing
[PeerJ]
2014
SOAPdenovo-Trans
SOAP transcriptome assembler
[Bioinformatics]
2014
SOAP3-dp
SOAP short-read aligner Gen3.5 - GPU-based
[PLoS ONE]
2013
COPE
Spaced-kmer based short-read error correction
[Bioinformatics]
2012
SOAPdenovo2
SOAP genome assembler Gen2 - Empirically improved memory-efficient
[GigaScience]
2012

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