Whole genome sequencing of Haemophilus influenzae NTHi strain HI2116
NTHi samples were prepared using 50-ng of total genomic DNA according to Nextera DNA library kit protocols (Illumina Inc). Samples were indexed according to standard protocols so that they could be pooled together and sequenced simultaneously in a single run on the Illumina MiSeq using paired-end 250-bp chemistry.  Prior to sequencing, all libraries were run individually on the Agilent High Sensitivity DNA chip to confirm library quality and average insert size.  Samples were pooled in equimolar amounts and 8pM of the pool was run on the sequencer.  Per Illuminas recommendation, 1% phiX control was spiked into the library pool prior to loading for quality control purposes. Thirty to forty million reads total were collected for each run.