Contribute to treangenlab/emu development by creating an account on GitHub.

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

Given a text, a query $\mathsf{rank}(q, c)$ counts the number of occurrences of character $c$ among the first $q$ characters of the text. Space-efficient methods to answer these rank queries form an i...

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

Despite being important ecological modulators of the gut microbiome, bacteriophage diversity and function remain under-characterized. We show that short-read metagenomic surveys can miss even globally highly prevalent viral family-level clusters (VFCs), that can be readily assembled and characterized with long-read metagenomic data from a relatively small cohort (n=109). While gut Bacteroidota phages have been the prevailing focus in the literature, we show that highly prevalent gut phage families frequently have Firmicutes hosts (termed GuFi phages), with broad host ranges verified using proximity-ligation (Hi-C) sequencing data. High-throughput sequencing of virus-like particles from fecal samples detected frequent enrichment of GuFi phages across samples, revealing their under-appreciated impact on the gut microbiome. We report the first in vitro induction and imaging of members of prevalent GuFi clades including the candidate orders Heliusvirales , Astravirales (VFC 2) and Suryavirales (VFC 4). Our findings underscore the importance of GuFi phages with broad host ranges in the gut microbiome, and the utility of long-read sequencing for viral discovery, paving the way for deeper insights into the role of bacteriophages in human health and disease. ### Competing Interest Statement IL is an employee of Phase Genomics. National Medical Research Council, 23-0614 National Research Foundation, NRFI09-0015 A*STAR, C210812044

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available protein structures, ...

Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont

a blog for miscellaneous bioinformatics stuff

Mirdita Lab builds scalable bioinformatics methods.

Openings

Changes #504: Introduce collinear chaining as the new default mapping and alignment method, replacing NAMs. This reproduces the Minimap2 chaining algorithm providing better mapping accuracy. NAMs ...

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru