TABLE 3.

Minimal quality parameters for Illumina sequencing of Salmonella isolates.

Parameter	Passing threshold
% of bases with a quality score > Q30 (%Q30)	2 × 301 bp: >70% 2 × 251 bp: >75% 2 × 151 bp: >80% 2 × 76 bp: >85%
Cluster passing filter	>75%
PhiX aligned	0.5–10%
PhiX error rate	<6%
Number of bases after trimming (per sample)	>150,000,000
Fraction of closest NCBI reference covered	>0.9
Number of contigs in de novo assembly	<300
N50 of the de novo assembly	>20,000
Average coverage of the de novo assembly	>30
Assembly length	4.5–5.5 Mb