HKUCS Bioinformatics Algorithms and Core Technology Research Laboratory

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31 repositories

Clair3-Nova
Public
de novo variant calling in trio using Nanopore long-reads
Python
•
BSD 3-Clause "New" or "Revised" License
•0•8•0•0•Updated Nov 1, 2024Nov 1, 2024
AutoPM3
Public
Python
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MIT License
•0•1•0•0•Updated Oct 30, 2024Oct 30, 2024
ClairS
Public
ClairS - a deep-learning method for long-read somatic small variant calling
bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels
Python
•
BSD 3-Clause "New" or "Revised" License
•7•72•2•0•Updated Oct 12, 2024Oct 12, 2024
ClairS-TO
Public
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina
Python
•
BSD 3-Clause "New" or "Revised" License
•3•49•3•0•Updated Oct 11, 2024Oct 11, 2024
Clair3-RNA
Public
Clair3-RNA - a long-read small variant caller for RNA sequencing data
rna-seq deep-learning nanopore rna variant-calling rna-editing rna-seq-pipeline ont long-read-sequencing pacbio-iso-seq
Python
•
BSD 3-Clause "New" or "Revised" License
•0•14•3•0•Updated Oct 8, 2024Oct 8, 2024
Clair3
Public
Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
deep-learning nanopore genomics computational-biology pacbio variant-calling illumina long-reads variant-detection ont-data
Python
•26•244•8•0•Updated Jul 29, 2024Jul 29, 2024
msdb-flask
Public
Mirtronstructdb: A comprehensive database of mirtrons with predicted secondary structures
HTML
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MIT License
•0•0•0•0•Updated Jul 28, 2024Jul 28, 2024
CellContrast
Public
CellContrast: Reconstructing Spatial Relationships in Single-Cell RNA Sequencing Data via Deep Contrastive Learning
bioinformatics single-cell-rna-seq spatial-transcriptomics contrastive-learning spatial-reconstruction
Jupyter Notebook
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MIT License
•0•5•0•0•Updated Jul 18, 2024Jul 18, 2024
Clair3-Trio
Public archive
Clair3-Trio: variant calling in trio using Nanopore long-reads
bioinformatics deep-learning nanopore genomics computational-biology variant-calling long-reads ont-models trio-variant-calling
Python
•
BSD 3-Clause "New" or "Revised" License
•1•14•2•0•Updated Apr 18, 2024Apr 18, 2024
ClusterV-Web
Public
C
•
BSD 3-Clause "New" or "Revised" License
•0•3•0•0•Updated Dec 27, 2023Dec 27, 2023
ClusterV
Public
ClusterV: finding HIV quasispecies and drug resistance from ONT sequencing data
bioinformatics nanopore hiv nanopore-sequencing hivdb subtype-finding
Python
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BSD 3-Clause "New" or "Revised" License
•0•10•2•0•Updated Dec 11, 2023Dec 11, 2023
Clair3-MP
Public
variant calling using with sequencing data from multiple platforms
Python
•
BSD 3-Clause "New" or "Revised" License
•2•4•2•0•Updated Jul 14, 2023Jul 14, 2023
SENSV
Public
A tool to detect structural variant
C
•
GNU Affero General Public License v3.0
•3•18•4•0•Updated Mar 27, 2023Mar 27, 2023
TC-RENO
Public
A tool to detect full length isoforms of RNA
Python
•3•3•0•0•Updated Dec 9, 2022Dec 9, 2022
CPG
Public
Building a Chinese pan-genome of 486 individuals
Python
•5•12•0•0•Updated Nov 23, 2022Nov 23, 2022
AF-NS
Public
Python
•1•1•0•0•Updated Nov 23, 2022Nov 23, 2022
ONT-TB-NF
Public
Comprehensive pipeline for detection of TB from ONT adaptive sequencing and amplicon data.
bioinformatics nanopore bioinformatics-pipeline mycobacterium-tuberculosis nanopore-analysis-pipeline adaptive-sequencing
Nextflow
•
BSD 3-Clause "New" or "Revised" License
•1•5•1•0•Updated Nov 22, 2022Nov 22, 2022
CONNET
Public
CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning
bioinformatics computational-biology genome-assembly deep-learning consensus
Python
•6•12•4•0•Updated Oct 28, 2022Oct 28, 2022
Clair
Public
Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling
bioinformatics deep-learning computational-biology variant-calling
Python
•
BSD 3-Clause "New" or "Revised" License
•12•104•2•1•Updated Sep 1, 2022Sep 1, 2022
MegaPath-Nano
Public
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
ont taxonomic-analysis amr-detection
C
•
BSD 3-Clause "New" or "Revised" License
•1•14•1•0•Updated Jul 2, 2022Jul 2, 2022
ECNano
Public
A target captured medical exome ONT sequencing with amplicon variant calling workflow
Python
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BSD 3-Clause "New" or "Revised" License
•1•6•0•0•Updated Mar 8, 2022Mar 8, 2022
MegaPath
Public
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data; MegaPath-Amplicon: filtering module for metagenomic amplicon data
filter ngs metagenomics amplicon taxonomic-classification
Java
•
BSD 3-Clause "New" or "Revised" License
•0•6•3•0•Updated Feb 10, 2022Feb 10, 2022
HKG
Public
Shell
•0•0•0•0•Updated Jan 11, 2022Jan 11, 2022
Chromatin-Fiber-Imaging
Public
Chromatin Fiber Imaging
Python
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GNU Affero General Public License v3.0
•0•1•0•0•Updated Jul 30, 2021Jul 30, 2021
ncov19_cytosine_depletion
Public
Python
•0•0•0•0•Updated Dec 11, 2020Dec 11, 2020
ChromSeg
Public
A framework for crossing-overlap chromosome segmentation
Python
•1•8•0•0•Updated Oct 23, 2020Oct 23, 2020
UNCALLED
Public
Raw nanopore signal mapper that enables real-time targeted sequencing
C++
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MIT License
•0•3•0•0•Updated Sep 7, 2020Sep 7, 2020
Translocator
Public
Translocator: local realignment and global remapping enabling accurate translocation detection using single-molecule sequencing long reads
C++
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GNU Affero General Public License v3.0
•0•13•1•0•Updated Jan 22, 2020Jan 22, 2020
Clairvoyante-PyTroch
Public
Pytorch version of Clairvoyante
Jupyter Notebook
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GNU Affero General Public License v3.0
•0•9•1•0•Updated Feb 28, 2019Feb 28, 2019
MegaGTA
Public
HMM-guided metagenomic gene-targeted assembler using iterative de Bruijn graphs
C++
•4•17•0•0•Updated Oct 3, 2016Oct 3, 2016