Qiandong Zeng

VCFCons: a versatile VCF-based consensus sequence generator for small genomes

VCFCons generates consensus sequences from VCF files with customizable filtering for SARS-CoV-2 surveillance, producing accurate sequences accepted by GISAID and NCBI.

A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

The paper develops a diploid assembly-based benchmark for variants in the MHC region using HG002 data, identifying 21496 small variants with high concordance to clinical HLA types.

Whole genome analysis illustrates global clonal population structure of the ubiquitous dermatophyte pathogen Trichophyton rubrum

The paper analyzes genome sequences of Trichophyton rubrum and Trichophyton interdigitale to show that T. rubrum is clonal with limited genetic variation and no evidence of sexual reproduction.

Comparative analysis highlights variable genome content of wheat rusts and divergence of the mating loci.

The paper compares the genomes of three wheat rust pathogens to identify gene content variation and divergence in mating loci, highlighting differences in genome size, heterozygosity, and effector expression.