HKUCS Bioinformatics Algorithms and Core Technology Research Laboratory

Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

Clair

Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

ClairS

ClairS - a deep-learning method for long-read somatic small variant calling

ClairS-TO

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

SENSV

A tool to detect structural variant

MegaGTA

HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs

MegaPath-Nano

MegaPath-Nano: Accurate Compositional Analysis and Drug-level Antimicrobial Resistance Detection Software for Oxford Nanopore Long-read Metagenomics; MegaPath-Nano-Amplicon: filtering module for metagenomic amplicon data

Clair3-Trio

Clair3-Trio: variant calling in trio using Nanopore long-reads

Translocator

Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads

CONNET

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning

CPG

Building a Chinese pan-genome of 486 individuals

Clairvoyante-PyTroch

Pytorch version of Clairvoyante

Clair3-RNA

Clair3-RNA - a long-read small variant caller for RNA sequencing data

ChromSeg

A framework for crossing-overlap chromosome segmentation

ClusterV

ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data

ECNano

A target captured medical exome ONT sequencing with amplicon variant calling workflow

MegaPath

MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data

ONT-TB-NF

Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.

Clair3-MP

variant calling using with sequencing data from multiple platforms

CellContrast

CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning

ClusterV-Web

TC-RENO

A tool to detect full length isoforms of RNA

UNCALLED

Raw nanopore signal mapper that enables real-time targeted sequencing

Clair3-Nova

de novo variant calling in trio using Nanopore long-reads

AF-NS

Chromatin-Fiber-Imaging

Chromatin Fiber Imaging

HKG

megabox

A web platform for hosting up-to-date MEGAHIT assemblies of publicly available but challenging metagenome sequence data.

ncov19_cytosine_depletion