| Summary: | Abstract Structural variants (SVs, including large‐scale insertions, deletions, inversions, and translocations) significantly impact the functions of genes in the microbial genome, and SVs in the microbiome are associated with diverse biological processes and human diseases. With the advancements in sequencing and bioinformatics technologies, increasingly, sequencing data and analysis tools are already being extensively utilized for microbiome SV analyses, leading to a higher demand for more dedicated SV analysis workflows. Moreover, due to the unique detection biases of various sequencing technologies, including short‐read sequencing (such as Illumina platforms) and long‐read sequencing (e.g., Oxford Nanopore and PacBio), SV discovery based on multiple platforms is necessary to comprehensively identify the wide variety of SVs. Here, we establish an integrated pipeline MetaSVs combining Nanopore long reads and Illumina short reads to analyze SVs in the microbial genomes from gut microbiome and further identify differential SVs that can be reflective of metabolic differences. Our pipeline provides researchers easy access to SVs and relevant metabolites in the microbial genomes without the requirement of specific technical expertise, which is particularly useful to researchers interested in metagenomic SVs but lacking sophisticated bioinformatic knowledge.
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