Weihua Pan

Reference-guided genome assembly at scale using ultra-low-coverage high-fidelity long-reads with HiFiCCL

HiFiCCL improves ultra-low-coverage genome assembly using high-fidelity long-reads, enhancing structural variant detection and pangenome construction in human and plant datasets.

CentIER: accurate centromere identification for plant genomes with sequence specificity information

CentIER identifies centromere regions in plant genomes using sequence specificity, achieving over 90% accuracy and providing insights into centromeric retrotransposons and tandem repeats in monocots and dicots.

Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes

This study benchmarks eleven HiFi assemblers on eukaryotic genomes and metagenomes, finding Hifiasm superior for complex genomes and Hifiasm-meta for metagenomes.

Reference-guided automatic assembly of genomic tandem repeats with only HiFi and Hi-C data enables population-level analysis

TRFill improves genome assembly of tandem repeats using HiFi and Hi-C data, enhancing completeness and enabling population-level analysis of subtelomeric repeats.

GFAP: ultra-fast and accurate gene functional annotation software for plants

GFAP is a software tool for plant gene annotation that uses a large database of 236 plant species to improve accuracy and speed.

CIDP: A multi-functional platform for designing CRISPR sgRNAs

CIDP is a CRISPR sgRNA design platform that allows users to input genomic sequences to design sgRNAs, minimizing off-target effects and offering additional functions for shared sgRNA identification and primer design.

OMGS: Optical Map-based Genome Scaffolding

OMGS improves genome scaffolding by utilizing multiple optical maps, achieving better contiguity and correctness than existing methods.

Validating genome-wide CRISPR-Cas9 function in the non-conventional yeast Yarrowia lipolytica

The paper validates genome-wide CRISPR-Cas9 function in Yarrowia lipolytica by quantifying sgRNA efficiency and identifying high-efficiency guides for 94% of genes.