Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly.

Draft genomes generated from Oxford Nanopore Technologies (ONT) long reads are known to have a higher error rate. Although existing genome polishers can enhance their quality, the error rate (including mismatches, indels and switching errors between paternal and maternal haplotypes) can be significant. Here, we develop two polishers, hypo-short and hypo-hybrid to address this issue. Hypo-short utilizes Illumina short reads to polish an ONT-based draft assembly, resulting in a high-quality assembly with low error rates and switching errors. Expanding on this, hypo-hybrid incorporates ONT long reads to further refine the assembly into a diploid representation. Leveraging on hypo-hybrid, we have created a diploid genome assembly pipeline called hypo-assembler. Hypo-assembler automates the generation of highly accurate, contiguous and nearly complete diploid assemblies using ONT long reads, Illumina short reads and optionally Hi-C reads. Notably, our solution even allows for the production of telomere-to-telomere diploid genomes with additional manual steps. As a proof of concept, we successfully assembled a fully phased telomere-to-telomere diploid genome of HG00733, achieving a quality value exceeding 50.

Lucio Phenomenon: A Rare Presentation of Hansen's Disease.

Lucio phenomenon (LP) is a rare reactional state seen in cases of diffuse lepromatous leprosy. Lucio leprosy is a pure, primitive, and diffuse form of lepromatous leprosy. It is observed almost exclusively in Mexico and Central America and is considered a globally restricted phenomenon. However, isolated cases are being reported worldwide. Patients with Lucio leprosy often present with manifestations of LP, which includes purpuric macules with multiple and extensive areas of ulceration with bizarre-patterned, angulated borders mainly affecting the extremities. LP is difficult to recognize, especially in nonendemic countries, which can lead to a delay in its diagnosis and management. We report a case of LP due to its occurrence in the classical form of lepromatous leprosy and rarity in North India.