Overview of detection methods

Repo for the main code associated with this work is available here

Use Serratus to perform a human

For a digest on how to screen all human viruses by all RNA-seq libraries in Serratus, check out the repo here for reproducing the pan-virus screen.

HHV-6B reference genome

We developed a kallisto|bustools workflow to rapidly quantify reads from either single-cell or bulk transcriptomes. We downloaded the GenBank AF157706 reference transcriptome and created a kallisto index using the default -k 31 (kmer) parameter. The best place for reproducing our HHV-6 pseudoalignment pipeline is here. For single-cell libraries, raw sequencing reads were processed using the kallisto bus command with appropriate hyperparameters for each version of the single-cell chemistry (either 14 or 16 bp sequence barcode and 10 or 12 bases of UMI sequence).

After barcode and UMI correction, a plain text sparse matrix was emitted, corresponding to unique HHV-6B reads mapping to individual cells in the single-cell sequencing library. For bulk libraries, the same index could be utilized with the standard kallisto quant execution.