VITAbasic v1.5: Smarter Data Input, Deeper Microbiome Insights, and Built-in Quality Awareness

High-resolution data analysis is where discovery begins. As part of the VITAseer analysis system, the VITAbasic module has always served as the analytical core that transforms raw single-cell sequencing data into interpretable biological meaning. Together with VITAprok (for prokaryotic data) and VITAeuk (for eukaryotic data), it forms the foundation of VITA’s end-to-end pipelines for both microbial and eukaryotic single-cell transcriptome analysis.

Now, with the launch of VITAbasic v1.5, that foundation has become even stronger. The new release focuses on user-driven flexibility, streamlined microbiome support, and transparent data quality evaluation—three elements that make the transition from raw reads to reliable insight smoother than ever.

1. Enhanced Input Flexibility: Tailored to How You Work

As the VITA user community continues to grow, researchers are increasingly interested in reanalyzing clean FASTQ data from previously published studies or developing customized workflows based on the VITA pipeline to meet specific experimental objectives. To address these evolving research needs, VITAbasic v1.5 introduces an upgraded analysis workflow that supports both raw and clean FASTQ inputs (Figure 1), offering greater flexibility and enabling more personalized analytical approaches.

This enhancement empowers users to select their preferred data format according to project design, ensuring seamless integration, reproducibility, and personalized data analysis across diverse research applications.

Figure 1. Input data types available in VITAbasic v1.5

2. Built-in Mouse Gut Microbiome Database: Precision for Animal Models

In the previous release (v1.4), VITAbasic came preconfigured with the UHGG reference database for human gut microbiome annotation. However, many research programs rely on mouse models, where reference quality has long been a limiting factor for taxonomic accuracy.

VITAbasic v1.5 now integrates the MGnify Mouse Gut reference genome as a default database, paired with optimized analytical parameters for improved classification precision (Table 1, Figure 2). Benchmarking demonstrated higher identification accuracy and consistency in mouse fecal microbiome datasets, enabling a standardized workflow for host–microbiome studies.

This upgrade expands the VITA platform’s utility beyond human samples—bringing single-cell microbial transcriptomics closer to the complexity of animal model research.

Table 1. Example data of a mouse fecal sample

Figure 2. UMAP visualization of a mouse gut microbiome dataset (species masked). Left: clustering of single bacterial cells based on transcriptomic profiles. Right: cluster annotation based on gene expression patterns (specific species names masked).

3. Built-in Risk Assessment: Greater Transparency in Data Quality

Not all samples are created equal—especially when working with FFPE tissues or partially degraded microbial materials. To help researchers make informed decisions about data usability, VITAbasic v1.5 introduces a new Risk Assessment module directly integrated into the HTML report (Figure 3).

This module evaluates multiple quality indicators to provide an at-a-glance overview of potential risks that may affect downstream data interpretation. The risk levels are categorized into three grades: Low, Medium, and High, offering users a clear and intuitive understanding of data reliability.

By quantifying uncertainty rather than concealing it, the platform promotes transparency and enables more confident, data-driven research decisions—particularly valuable when dealing with irreplaceable or challenging samples such as FFPE or low-quality microbial materials.

Figure 3. Risk assessment in the html report

VITAbasic v1.5 also incorporates numerous backend optimizations and bug fixes reported by users. The result is a more stable, responsive, and intuitive experience—from data upload to visualization output.

Looking Ahead

With its new level of flexibility, microbiome intelligence, and quality awareness, VITAbasic v1.5 reinforces the analytical strength of the VITAseer suite. It empowers researchers to go beyond surface-level data exploration and focus on biological interpretation—whether investigating FFPE tumor heterogeneity or microbiome function in preclinical models.

The VITA platform will continue to evolve alongside the community, driving single-cell and spatial multi-omics innovation—one upgrade at a time.