| ClairS-TO | (2024) ONT somatic variant caller for tumor-only samples |
| ClairS | (2023) ONT somatic variant caller for paired tumor-normal samples |
| ClusterV | (2023) Find HIV quasispecies and drug resistance using ONT sequencing data [Clin. Chem] [Bioinform. Adv.] |
| ONT-TB-NF | (2023) A Nextflow pipeline to process ONT adaptive sequencing data for TB antibiotic-resistance detection [Scientific Reports] |
| Duet | (2022) SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing [BMC Bioinformatics] |
| Clair3-Trio | (2022) ONT family trio variant caller [Briefings in Bioinformatics] |
| Clair3 | (2022) ONT small variant caller Gen3 [Nature Computational Science] |
| SENSV | (2022) Detecting structural variations with precise breakpoints using low-depth WGS data from a single oxford nanopore MinION flowcell [Scientific Reports] |
| ECNano | (2022) A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell [BMC Medical Genomics] |
| HKG | (2022) Variant database with 205 Hong Kong Cantonese exomes [NAR Genomics and Bioinformatics] |
| RENET2 | (2021) Full-text Gene-Disease Relation Extraction [NAR Genomics and Bioinformatics] |
| CONNET | (2020) Improving ONT data genome assembly consensus quality [iScience] |
| Clair | (2020) ONT small variant caller Gen2 [Nature Machine Intelligence] |
| RENET | (2019) A Deep Learning Approach for Extracting Gene-Disease Associations from Literature [RECOMB 2019] |
| Clairvoyante | (2019) ONT small variant caller Gen1 [Nature Communications] |
| 16GT | (2017) Small variant caller using a 16-genotype probabilistic model [GigaScience] |
| LRSim | (2017) Linked-Reads Simulator [Comput Struct Biotechnol J] |
| BASE | (2016) An assembly method for large genomes using longer NGS reads [BMC Genomics] |
| MICA | (2015) Fast short-read aligner that uses Intel MIC [BMC Bioinformtics] |
| MEGAHIT | (2015) Fast and memory-frugal metagenomics assembler [Bioinformatics] |
| database.bio | (2015) A web application for interpreting human variations [Bioinformatics] |
| BALSA | (2014) Integrated secondary analysis for whole-genome and whole-exome sequencing [PeerJ] |
| SOAPdenovo-Trans | (2014) SOAP transcriptome assembler [Bioinformatics] |
| SOAP3-dp | (2013) SOAP short-read aligner Gen3.5 [PLoS ONE] |
| COPE | (2012) Spaced-kmer based short-read error correction [Bioinformatics] |
| SOAPdenovo2 | (2012) SOAP genome assembler Gen2 [GigaScience] |