Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.

ABSTRACT: The metagenome analysis of complex environments with thousands of datasets, such as those in the Sequence Read Archive, requires substantial computational resources for it to be completed within a reasonable time frame. Efficient use of infrastructure is essential, and analyses must be fully reproducible with publicly available workflows to ensure transparency. Here, we introduce the Metagenomics-Toolkit, a scalable, data-agnostic workflow that automates the analysis of short and long metagenomic reads from Illumina and Oxford Nanopore Technology devices, respectively. The Metagenomics-Toolkit provides standard features such as quality control, assembly, binning, and annotation, along with unique capabilities including plasmid identification, recovery of unassembled microbial community mem

SUBMITTER: Belmann P 

PROVIDER: S-EPMC12267984 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature