RT Journal Article
SR Electronic
T1 Ultra-efficient, unified discovery from microbial sequencing with SPLASH and precise statistical assembly
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.01.18.576133
DO 10.1101/2024.01.18.576133
A1 Henderson, George
A1 Gudys, Adam
A1 Baharav, Tavor
A1 Sundaramurthy, Punit
A1 Kokot, Marek
A1 Wang, Peter L.
A1 Deorowicz, Sebastian
A1 Carey, Allison F.
A1 Salzman, Julia
YR 2024
UL http://biorxiv.org/content/early/2024/01/22/2024.01.18.576133.abstract
AB Bacteria comprise > 12% of Earth’s biomass and profoundly impact human and planetary health.1 Many key biological functions of microbes, and functions differentiating strains, are conferred or modified by genome plasticity including mobilization of genetic elements, phage integration, and CRISPR arrays. Characterizing each of these processes is time-consuming and requires custom bioinformatic workflows ill-suited to enable discovery of new sources of genetic diversity or to uncover which elements are active. Further, strain typing of bacterial species and approaches to discriminate sub-populations remain time-consuming and resource intensive. Here, we show that SPLASH, our published approach for reference-free discovery and analysis directly from raw reads, and an improved statistical assembly algorithm, compactors, unify diverse tasks in microbial sequence analysis: discovering new mobile elements and CRISPR arrays missing from any reference, and generating rapid, metadata-free strain typing of diverse bacteria. SPLASH and compactors together constitute a new general discovery tool for biological discovery in the microbial world.Competing Interest StatementThe authors have declared no competing interest.