What are the causes of low read counts from an Illumina MiSeq™ run?

Low clustering possible causes (1200 to 1400 K/mm2 expected for Illumina MiSeq v3):

– Imprecise quantification of final libraries

– Inaccurate dilution/mixing of libraries before loading

– Denaturation issues

– Insufficient mixing of the MiSeq reagent cartridge (normally requires 10x inversion once thawed)

High clustering possible causes:

– Imprecise quantification of final libraries

– Inaccurate dilution/mixing of libraries before loading on the MiSeq