Rayan Chikhi

Abstract Genome-wide Association Studies (GWAS) have played a crucial role in uncovering the genetics underlying complex human traits. Recently, there has been considerable interest in adapting GWAS-like methodologies to investigate pathogenic bacteria. Despite the variety of methods proposed, there remains a lack of clarity on how to effectively model the intricate population structures found in bacterial cohorts.

Abstract Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables.

Abstract Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as the Basic Local Alignment Search Tool (BLAST) and its successors.