Download Sample Report Data

Overview

You can easily download data from the Sample Report page, including sequences and alignment metrics, for downstream analysis. Here we describe how to download data and available files.

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Download Data

To download data, click the Download button in the right-hand corner of the Sample Report page and select the appropriate file from the dropdown menu. You can download files from the Table and Tree views. If you click the Download button from the Tree View, you will be able to download images of the taxon tree. You can also download read and contig sequences that aligned to taxa of interest directly from the Sample Report Table.

Available Files for Download from Table View:

• • Report Table: Sample Report Table values for all detected taxa in CSV format.
  • Report Table with Applied Filters: Sample Report Table values for taxa passing applied filters in CSV format.
  • Non-Host Reads: All unique read sequences (i.e., deduplicated) that passed QC, host, and human filters in FASTA format.
  • Non-Host Contigs: All assembled contig sequences in FASTA format.
  • Non-Host Contig Summary: General contig metrics (e.g, contig lengths and number of reads mapping to the contig) and accession IDs for their top matches in the NT and NR databases (CSV format).
  • Unmapped Reads: All non-host read sequences (non-deduplicated) that didn't align to the NT and NR databases in FASTA format.
  • Intermediate Files:
    • Results Folder: Select "View Results Folder" to navigate to a page containing all the intermediate files generated during sample processing. Download intermediate files of interest by clicking the filename.
    • Pipeline Visualization: Select "View Pipeline Visualization" to navigate to an interactive schematic of the pipeline workflow. Click on any step of interest to view details and download generated files.

Available Files for Download from Taxonomic Tree View:

• • All available files from the Sample Report Table View (listed above).
  • Taxon Tree as SVG: Taxon tree image in SVG format.
  • Taxon Tree as PNG: Taxon tree image in PNG format.

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Download Sequences Matching Taxa of Interest

To download sequences of interest from the Sample Report Table:

1. Hover over the taxon row and click the Download icon.

2. Select contigs or reads from the dropdown menu (both files are downloaded in FASTA format).