Interactive summary¶

The Interactive Summary report is a great way to get a high-level overview of the results for all your samples that were submitted in a single analysis. At the top of the report, you will see an LLM-generated summary, which provides a high-level overview of the results from key sections of the summary report.

General stats table¶

The General Statistics table provides a high-level overview of the QC metrics for each sample in a given analysis. Here, you will find the isolate identification result (if “Isolate” was selected as the sample type), details on the assembly for each sample (length, median contig length - N50, median genome coverage, and the number of reads that passed BugSeq’s QC filters (see the Quality Control section below for more details). You can also configure the columns to add or remove additional metrics by clicking “Configure Columns” at the top of the table, or you can export the whole table as a CSV file by clicking “Export as CSV”.

Metagenomic classification¶

The “Top Taxa” bar chart provides a high-level overview of the metagenomic classification results for all samples in a given analysis. Hovering over each plot provides additional information on the read counts assigned to the top 10 taxa across all samples in an analysis. Clicking the buttons on the top of the plot allows you to configure between read counts and percentages, as well as visualize the plot for other taxonomic ranks like genus or family.

More detailed metagenomic classification results can be seen in the Per-Sample Reports or the Metagenomic Classification Reports sections of our docs.

AMR & plasmid analysis¶

In the Interactive Summary, you will find several tables providing a summary of the AMR results for your analysis. In the “Genotypic Determinants” table, you will find the results for each AMR genotypic determinant found in your analysis, as well as the samples where each determinant was found. Please see the AMR section of our docs for more information on BugSeq’s approach to AMR.

Below this table, you will find a phenotypic AMR analysis, showing the sample IDs and organism name as the column headers, and antimicrobial drug and drug class that each organism is predicted to be resistant to.

Below the AMR analysis, you will find two tables providing results from BugSeq’s plasmid analysis. In the first table you will find the plasmids (Cluster IDs) associated with each sample ID. These plasmid Cluster IDs are like taxonomic identifiers and are stable across time. Cluster IDs are generated separately from bacterial host identification and therefore may be used to track plasmid spread across species. Novel plasmids not found in the BugSeq database are labelled “Novel_-like”. The second table provides the list of plasmids, along with QC metrics related to the coverage for each plasmid, the predicted host range, and the AMR genotypic determinants that were found on each plasmid, which can be used to infer transmission events.

Virulence factors, MLST, and pathogen-specific analyses¶

BugSeq automatically looks for certain clinically-important virulence factors and performs pathogen-specific analyses, for example, Klebsiella pneumoniae hypervirulence typing, depending on the composition of the submitted samples. These results can all be found in the Interactive Summary report. For a full list of supported analyses, see the support analyses page.

BugSeq also performs MLST analysis for all organisms where there is a MLST scheme available.

Quality control¶

Sequencing data¶

Quality is assessed before any preprocessing. The most important graph is the Quality Control Status Checks.

As with a stop light, green boxes reflects high quality data, yellow reflects a warning, and red reflects concern. Thresholds for this graph are custom tailored to your sequencing platform and experimental design. For example, nanopore sequences will flag as a warning if the average Per Sequence Quality (measured in Phred score) is below Q8, whereas Illumina sequences will flag if below Q20.

For a full description of graph content, please see the FastQC manual.

Assemblies¶

Basic statistics¶

Basic assembly statistics, such as N50 and total length, are calculated with QUAST. We refer the reader to the QUAST interpretation guide for details on assembly plots and statistics in the BugSeq per-sample reports.

Bin completeness¶

Bin completeness is assessed with BUSCO. We refer the reader to the BUSCO interpretation guide for details on the BUSCO plots contained in the BugSeq per-sample reports.