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Other reports

BugSeq outputs several other report formats depending on the analysis parameters under the “Other” tab of the results page.

Genome coverage plots

For metagenomic analyses, BugSeq outputs plots detailing the horizontal genome coverage for all taxa that reads were classified to in a genome. The reads are aligned against the NCBI reference genome for each taxa. These plots can be useful in determining whether an organism is truly present in a sample (multiple genome regions covered), or if the classification was likely due to contamination or amplification artifacts introduced during the library preparation protocols.

Note

In cases where the NCBI RefSeq reference genome is fragmented, BugSeq will align the reads against the individual contigs of the genome assembly. This will result in multiple plots that can be navigated by clicking on individual contigs that make up the fragmented genome.

Interactive genome coverage visualizations

Bacterial isolate summary

For all analysis submitted under the “Isolate” sample type, BugSeq outputs an Excel (XLSX) formatted summary file for all isolates in a given analysis. This file is designed to provide a high-level summary of each isolate in an analysis and contains the following information:

  • Isolate identification & NCBI Taxonomy ID
  • Assembly completeness
  • Detected AMR (phenotype and genotype) & Plasmids
  • Number of contigs and coverage of the assembly relative to the reference genome
  • Percent identity of the assembly relative to the reference genome
  • Assembly length and GC content warnings (see Labs for more details on configuring QC thresholds for isolates.
  • Peak insert size
  • Average read quality scores

Example isolate summary table

Sample Name Taxon TaxId Assembled Assembly Completeness % Assembly Duplication Molecule Type AMR Genotypic Determinants Plasmids % of Coverage to Reference Length QC GC Content QC Average Quality R1 Average Quality R2 Average Read Quality Average Read Quality Peak Insert Size
Sample_1 Proteus mirabilis 584 TRUE 99.2% 0.0% DNA Amikacin, aac(3)-IIe, AA190, AA 99.27% Warn Pass 59 37.22 36.23 36.73 322
Sample_2 Proteus mirabilis 584 TRUE 99.2% 0.0% DNA Amikacin, aac(3)-IIe, AA190, AA 99.29% Warn Pass 84 35.41 34.69 35.05 343
Sample_3 Proteus mirabilis 584 TRUE 99.2% 0.0% DNA Amikacin, aac(3)-IIe, AA190, AA 99.27% Warn Pass 44 37.33 36.39 36.86 343

Syndromic panel reports

For certain sample types and platforms, BugSeq outputs syndromic panel reports that provide a qualitative pathogen detection summary for a defined set of validated pathogens. As with all BugSeq reports, the pipeline version is displayed at the top of the report, and the reports are immutable for use in regulated environments.

BugSeq harnesses machine learning techniques trained on publicly available datasets with known ground truth to define reporting thresholds for a defined list of reportable pathogens in these reports. Currently, BugSeq has trained thresholds for reporting pathogens in the following sample types and platforms:

  • Oxford Nanopore:
    • Lower respiratory, for example, BAL
    • Upper respiratory, for example, nasopharyngeal swabs
  • Short-Read (like Illumina):
    • Cerebrospinal fluid (CSF)
    • Upper respiratory, for example, nasopharyngeal swabs
Failure to make a pathogen detection prediction?

An “N/A” value for a pathogen detection may be present in cases where BugSeq is unable to compute a value for a variable necessary for pathogen prediction that’s defined in the trained BugID model for that sample type. Please reach out to support if you encounter unexpected results.

Want to train thresholds for your specific application?

BugSeq is happy to work with individual laboratories and diagnostic manufacturers to train mNGS-based pathogen reporting models to suit your specific application. Reach out to us at contact@bugseq.com to schedule a call to discuss your specific application of interest.

MycoSNP (Candida auris)

In addition to BugSeq’s own refMLST Outbreak Analysis tool, which supports Candida auris, BugSeq also supports CDC’s MycoSNP tool. BugSeq performs clade-specific MycoSNP analysis using the reference genome for each C. auris clade. Additionally, BugSeq outputs the following files from MycoSNP:

  • Excel (xlsx) formatted distance matrix
  • FastTree phylogeny (NH)
  • IQ Tree phylogeny (NH)
  • QuickSNP phylogeny (NWK)
  • Rapid NJ phylogeny (NH)
  • Variant calling (VCF) file for each submitted isolate