Details of HT-SGS data analysis.

(A) Bioinformatic pipeline, depicting sequential workflow steps and tools used. Black boxes show tasks at each step, with the tools used in the grey boxes, and the outputs in the blue bubbles. (B) Initial exclusion of false UMI bins based on read count distribution on a log scale. The dashed line indicates the read count inflection point below which UMI bins in this sample were excluded. (C) Final exclusion of low count UMI bins based on read count distribution on a log scale. The dashed line indicates the read count knee point below which UMI bins in this sample were excluded, following initial false bin removal from the sample and network adjacency. Data are presented for the cultured virus sample presented in Fig 2.

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