DRAGEN Targeted Microbial

Supported hybrid-capture enrichment panels

• Viral Surveillance Panel (VSP)
• Pan-Coronavirus Panel (Pan-Cov)
• Respiratory Virus Oligo Panel (RVOP)

Supported amplicon primer schemes on Protocols.io or ARTIC Network

• Universal Influenza A/B (Zhou et al / Ying Lin)
• MPXV (Grubaugh Lab)
• Dengue 400 bp (Grubaugh Lab)
• RSV (Barr Lab / Ying Lin)
• SARS-CoV-2 ARTIC v3, v4, v4.1, v5.3.2(ARTIC Network)

Analysis Pipeline

1. Reads are trimmed and filtered using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW: 4:15 MINLEN:36.
2. Human reads are removed with a modified version of the SRA Human Read Scrubber tool.
3. MEGAHIT is used to perform de novo assembly on the scrubbed reads.
4. CD-HIT-EST is used to cluster similar contigs to reduce redundancy.
5. The resulting contigs are mapped to a set of reference genomes using minimap2.
6. The best matching reference for each contig is selected for short read mapping.
7. The scrubbed reads from step 3 are aligned to the selected reference genomes using [DRAGEN v4.0.3]
8. Sequence variants are called from the alignments using DRAGEN Somatic v4.0.3 and applied to the corresponding reference sequences to create consensus sequences.
9. If applicable, Pangolin and/or Nextclade are run on the consensus sequences.

Outputs

The software generates sequences representing a best estimate of the population of targeted sequences in the sample. NextClade and Pangolin analysis are run on select organisms. Output details in output txt file.