The study provides a quantitative basis for selecting MEGAHIT k-mer parameters according to whether computational efficiency or functional gene discovery is the primary aim, and indicates that reduced k-mer sets can lower computational cost but may miss biologically relevant functional signal, depending on the dataset and downstream target.
Metagenomics enables the recovery of metagenome-assembled genomes (MAGs), providing access to the metabolic potential of uncultured microbial communities that drive ecosystem function and biogeochemical cycles. However, as MAGs datasets increase in size and complexity, comparing functional repertoires and identifying e...
Karla P. López-Martínez, S. Hereira-Pacheco, Diana Hernández-Oaxaca et al.· Frontiers in Bioinformatics· 0 citations
By linking ARGs to their wider genetic contexts and hosts, the findings shed light on the previously unrecognized carriers of resistance genes in wastewater, and provides a valuable methodology for early identification of newly arising ARGs and their hosts.
Melina A. Markkanen, Heidi Putkuri, D. Kičiatovas et al.· Genome Biology· 0 citations
While shotgun metagenomics is often used to profile antibiotic resistome in gut microbial communities, few studies have investigated if the choice of sequencing platform and assembly strategy affect what mobile genetic elements and antimicrobial resistance genes are recovered. In this study, we compared three platforms...
Dabin Jeon, Tatsuya Unno· Journal of Microbiology· 0 citations
The MiDAS genome catalog provides a framework for linking taxonomy, metabolism and ecological roles in wastewater treatment systems globally and enables analyses of predicted functional traits and their ecological context.
Lei Liu, C. Singleton, R. Kirkegaard et al.· bioRxiv· 1 citation
A standardized workflow for multiplexed amplicon sequencing from sample collection through data analysis for diverse sample types that produces data and publication-ready figures for multiple taxonomic and functional genes for carbon, nitrogen, phosphorus, sulfur, and arsenic cycling for each sample analyzed is develop...
Alexa J. Bennett, Ryan M. Moore, Craig W. Herbold et al.· bioRxiv· 0 citations
antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of ant...
Caner Bağcı, Kai Blin, N. Ziemert· bioRxiv· 1 citation· ⚡1
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