🔎Additional analysis

Consensus sequences generated by the app can be provided as input to various third-party tools for further analysis. For example, tools like Nextclade and Pangolin provide phylogenetic information (e.g. clade, lineage) based on comparisons to databases of known sequences. Similarly, tools like NCBI BLAST (Basic Local Alignment Search Tool) find annotated sequences in their databases that best match your sequences.

Nextclade

Output consensus sequences can be directly uploaded as input to Nextclade web app or command-line tool to conduct viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.

By default, the DRAGEN Microbial Amplicon app runs Nextclade on the app's output consensus sequences for the microorganisms and datasets listed below. The results are displayed in the BaseSpace reports.

Microorganism	Nextclade official datasets
Dengue	Dengue virus All serotypes (nextstrain/dengue/all)
	Influenza A H1N1pdm HA (nextstrain/flu/h1n1pdm/ha/MW626062) Influenza A H1N1pdm NA (nextstrain/flu/h1n1pdm/na/MW626056)
	Influenza A H3N2 HA (nextstrain/flu/h3n2/ha/EPI1857216) Influenza A H3N2 NA (nextstrain/flu/h3n2/na/EPI1857215)
	Influenza B Victoria HA (nextstrain/flu/vic/ha/KX058884) Influenza B Yamagata HA (nextstrain/flu/yam/ha/JN993010) Influenza B Victoria NA (nextstrain/flu/vic/na/CY073894)
Mpox Clade I	Mpox virus (Clade I) (nextstrain/mpox/clade-i)
	Mpox virus (All clades) (nextstrain/mpox/all-clades) Mpox virus (Clade IIb) (nextstrain/mpox/clade-iib)
RSV A	RSV-A (nextstrain/rsv/a/EPI_ISL_412866)
RSV B	RSV-B (hnextstrain/rsv/b/EPI_ISL_1653999)
SARS-CoV-2	SARS-CoV-2 (nextstrain/sars-cov-2/wuhan-hu-1/orfs)

There may be Nextclade datasets that are applicable to your consensus sequences but not listed above (see all available datasets here). In such cases, you can run Nextclade with your consensus sequences and the dataset of your interest using either the Nextclade web app or command-line tool.

Please see Nextclade documentation for more information.

Pangolin

Output consensus sequences can be directly uploaded as input to Pangolin web app or command-line tool to assign SARS-CoV-2 sequences to global lineages.

By default, the DRAGEN Microbial Amplicon app runs Pangolin for all SARS-CoV-2 consensus sequences and displays the results in the BaseSpace reports.

Please see Pangolin documentation for more information.

NCBI BLAST

Output consensus sequences can be directly uploaded to NCBI BLAST to find similar sequences in NCBI's large reference database, which is updated frequently to include recently generated sequences. BLAST is available on the NCBI website and also as a standalone command-line tool.

If available and applicable, output contig sequences from the DRAGEN Microbial Amplicon app may also be uploaded to BLAST. This may be useful if the reference genome reported by the app does not match your expectation. BLAST may find a better reference genome, which can be uploaded as custom reference to the app.

Please see NCBI BLAST help page for more information.