Chuan-Le Xiao

NECAT. Nanopore data assembler

MECAT. MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

MECAT2. C

Falign. An effective alignment tool for long noisy 3C data (e.g. Pore-C and C-walk)

hifimeth. High-fidelity 5mC DNA methylation detection model for PacBio HiFi reads

DeepPlant. We developed DeepPlant, a highly accurate plant methylation detection model, demonstrating a significant performance improvement. DeepPlant was evaluated on species with varying CHH methylation levels, achieving a high correlation of 70%-88% with BS-seq in CHH methylation quantification, outperforming Dorado by over 10%.

dip3d. A fast and effective high-order diploid human 3D genome construction method

DeepBAM. High-fidelity 5mCG DNA methylation detection model for Nanopore sequencing reads

Z-Calling. Z-Calling is a machine-learning based tool for (1) distinguishing dZ-DNA molecules from ordinary DNAs and (2) calling Z bases in A/Z-coexisting DNAs. Z-Calling also has implemented a pipeline for detecting taxonomic or sequence sources of dZ-DNAs in mixed datasets.

Bream. Open-source and integrated base calling and methylation detection for a novel nanopore sequencing platform

Falign2. Alignment toolkit for Pore-C sequencing reads

lesv. High accuracy structural variations caller for Nanopore noisy long reads