COVIDSeq timing and logistics
What is the turnaround time for library preparation and sequencing?
Library preparation time varies based on number of samples processed, extraction method, and thermal cyclers and techs available. See the Illumina COVIDSeq RUO Kits Reference Guide for incubation times per step.
1536 to 3072 results can be sequenced in 12 hours on NovaSeq 6000 system using two SP or S4 reagent kits, respectively or 384 results in 12 hours using NextSeq 2000 P2 v3 reagent kits or NextSeq 500/550/550Dx (in Research Mode) HO reagent kit.
What is the recommended number of samples that can be sequenced per run?
MiSeq v2 flow cell: 30 samples per flow cell.
MiSeq v3 flow cell: 48 samples per flow cell.
MiniSeq HO flow cell: 48 samples per flow cell.
NextSeq 500/550 or 550Dx HO flow cell: 384 samples per flow cell.
NovaSeq 6000 system SP flow cell: 384 samples per lane and 768 total samples per flow cell.
NovaSeq 6000 system S4 flow cell: 384 samples per lane and 1536 total samples per flow cell.
NextSeq 1000/2000 P2 flow cell: 384 samples per flow cell.
Note: Lower pooling numbers are acceptable for surveillance use only.
How many operators are needed for this workflow?
This highly depends on sample pull through and proficiency of lab. It is reasonable that one experienced tech could manually process 384 samples in two days, given the appropriate equipment is available (eg, multichannel pipettes, thermal cyclers, etc.). Due to plating requirements and lengthy time of ARTIC PCR, the number of thermal cyclers is often a bottleneck.
How long can libraries be stored prior to sequencing?
Up to 30 days at -20°C. Illumina recommends sequencing libraries as soon as possible after pooling.
For more information, see:
Illumina COVIDSeq RUO Kits Reference Guide
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