Selected Software Packages

ClairS (2023) ONT somatic variant caller for paired tumor-normal
ClusterV (2023) Find HIV quasispecies and drug resistance using ONT sequencing data
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] (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]