TL;DR
PALACE, a conjugate-graph-based framework for assembling high-quality phage genomes from metagenomes, incorporates homology-based and deep-learning-based methods to detect phage signals and constructs a conjugate graph from the metagenomic sample.
MetaCAT outperforms existing methods in both clustering accuracy and computational efficiency across diverse datasets and provides a scalable framework for microbial community profiling and advances the understanding of host-microbe interactions.
PHORAGER (Prophage Hunting, vOtu Retrieval, Annotation and Genomic ExploRation), a scalable Nextflow pipeline for the standardised identification and quality assessment of prophages from bacterial genomes, validated using 30,824 publicly available ESKAPE pathogen genomes.
Applications across healthcare, environmental science, agriculture, biotechnology, and industry are reviewed with particular emphasis on clinical metagenomic next-generation sequencing (mNGS) for infectious disease diagnostics, antimicrobial resistance (AMR) surveillance, gut microbiome research, and precision medicine...
The GenomeCompendium is released, a public database and interactive analysis tool for complete prokaryotic genomes and it is shown that complex, repeat-rich genomes are more common than previously estimated.
This work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.
By introducing support for ancient DNA data in nf-core/mag, this paper aims to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.
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