Šikić lab
A computational group with a focus on the development of new algorithms and AI models for the analysis of DNA and RNA sequencing data and biomolecular strucures
Singapore
Pinned Repositories
GNNome
A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.
graphmap2
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
I002C
Telomere-to-Telomere diploid Indian Genome
ra
Assembler for raw de novo genome assembly of long uncorrected reads.
racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
raven
De novo genome assembler for long uncorrected reads
RiNALMo
RiboNucleic Acid (RNA) Language Model
rockfish
roko
A deep learning consensus polisher
Šikić lab's Repositories
lbcb-sci/raven
De novo genome assembler for long uncorrected reads
lbcb-sci/racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
lbcb-sci/herro
HERRO is a highly-accurate, haplotype-aware, deep-learning tool for error correction of Nanopore R10.4.1 or R9.4.1 reads (read length of >= 10 kbps is recommended).
lbcb-sci/graphmap2
GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1
lbcb-sci/RiNALMo
RiboNucleic Acid (RNA) Language Model
lbcb-sci/ra
Assembler for raw de novo genome assembly of long uncorrected reads.
lbcb-sci/GNNome
A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.
lbcb-sci/rockfish
lbcb-sci/I002C
Telomere-to-Telomere diploid Indian Genome
lbcb-sci/roko
A deep learning consensus polisher
lbcb-sci/ScaRa
SCARA - scaffolding with long reads
lbcb-sci/MetagenomicsBenchmark
lbcb-sci/ram
lbcb-sci/ratlesnake
lbcb-sci/Rockfish-old
Deep learning based method for detecting DNA base modifications
lbcb-sci/GNNs-Hamiltonian-cycles
Supplementary code for "Finding Hamiltonian cycles with graph neural networks"
lbcb-sci/heron-raven
Development of Raven - Heron branch
lbcb-sci/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
lbcb-sci/merlion
lbcb-sci/NeuralLayout
A GNN model that executes simplification algorithms used in the layout phase of de novo genome assembly process.
lbcb-sci/RNAseqEval
A tool for evaluating RNA seq mapping
lbcb-sci/T2T-assemblies
T2T assemblies of human and durian genomes
lbcb-sci/tarantula