Reliable and accurate diagnostics from highly multiplexed sequencing assays

Scalable, inexpensive, and secure SARS-CoV-2 testing is crucial for pandemic control, and highly multiplexed sequencing assays are promising alternatives to RT-qPCR tests. Their clinical use requires reliable analysis, interpretation, and computational workflows that handle sample indices, biological targets, gene counts, and infection-status classification. A kallisto-bustools workflow processes recently proposed sequencing-based diagnostic tests quickly and with low memory, validates SwabSeq analysis against an orthogonal workflow, and extends to assays with different targets and sample-index structures.