Chromosome-Level Haplotype Assembly for .

Haplotype provides significant insights into understanding genomes at both individual and population levels. However, research on many non-model organisms is still based on independent genetic variations due to the lack of haplotype. We conducted haplotype assembling for , a non-model organism that plays a vital role in human civilization.

Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic.

SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerging SARS-CoV-2 variants could increase transmissibility and diminish vaccine protection. However, whether coinfection with multiple SARS-CoV-2 variants exists remains controversial.

SpecHap: a diploid phasing algorithm based on spectral graph theory.

Haplotype phasing plays an important role in understanding the genetic data of diploid eukaryotic organisms. Different sequencing technologies (such as next-generation sequencing or third-generation sequencing) produce various genetic data that require haplotype assembly. Although multiple diploid haplotype phasing algorithms exist, only a few will work equally well across all sequencing technologies.