Neng Huang

compleasm. A genome completeness evaluation tool based on miniprot

longcallR. longcallR is a tool for SNP calling, haplotype phasing, and allele-specific analysis with long-read RNA-seq data.

NanoSNP. A deep learning-based SNP calling method to identify SNPs based on low-coverage Nanopore sequencing reads.

BlockPolish. BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer

SACall-basecaller. Python

longcallR-nf. Nextflow

NeuralPolish. NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.

longcallR-nn. longcallR_nn is a variant caller specifically designed for long-read RNA-seq data, utilizing a ResNet50 model.

PrimFilt. A long-read RNA-seq internal priming detection and filtering tool

rust-fastqtl. A Rust reimplementation of the core FastQTL cis-QTL mapping logic.

longcallR_scripts. Jupyter Notebook

variant_detection_nf. Nextflow

BPFGM. BlockPolish feature generation module (BPFGM) is used to divide the draft assembly into blocks from reads-to-assembly alignment and generate feature matrices used for predicting consensus sequence.