🌀How to set up and run an analysis

1. Launch the DRAGEN 16S Plus BaseSpace app, which can be found in the "Dragen" and "Infectious Disease + Microbiology" app collections.

2. Enter a name for the Analysis.

3. Choose either "Project" or “Biosample list” as input type. When a Project is selected, the app will attempt to find all FASTQ files in that Project and run analyses on them.

4. Select a reference database. Only one database can be selected per analysis. If "Custom Database" is selected, the "Custom database specification" section is enabled to allow entry of a custom reference FASTA for taxonomic classification. See Custom database FASTA file format for further details.

5. Analysis Options:

• Perform read QC (Quality Control)

  • If checked, reads are pre-processed using quality metrics before analysis. For paired-end data, both read1 and read2 must pass QC filtering for the read pair to be used for analysis.

  • If unchecked, read quality metrics are calculated, but reads are not trimmed or filtered before analysis.

1. Specify a "Read count threshold". The read count threshold is a reporting threshold representing the number of reads (or read pairs for paired-end data) that must be classified to a taxonomic identifier for the taxonomic identifier to be included in summary reports. It is an integer with a valid range of 0 to 1000, inclusive. The default value is 0, meaning that no filtering is applied to results and all taxa with classified reads are reported.

2. Select the Project where the Analysis Output should be saved.