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VPipe standard analysis pipeline: VPipe takes raw FASTQ data generated by Illumina or Ion Torrent sequencing instruments. Raw reads are processed using the Read Quality and Trimming module prior to de novo assembly using SPAdes and detection of viral contigs via BLASTN. Analysis results are available on the VPipe user interface, accessible through the CDC OAMD portal. For SARS-CoV-2 data sets, reference-based assembly is also run in parallel with the de novo Assembly Module.
