Shotgun Metagenomics Sequencing

We use Illumina technology and aim for at least 1 million reads per sample. However, we cannot guarantee the success of NGS procedures as this technique is the unbiased amplification of all nucleic acids in the sample. The number of reads for a pathogen of interest may not be sufficient to produce a full genome. In those instances, a draft genome may be produced and additional sequencing may be necessary to fill in gaps in the genome. Additional sequencing options and costs will be discussed if needed.

In metagenomic sequencing, failure to identify a pathogen is not a guarantee that the pathogen is absent. False-negative results may occur in metagenomic sequencing for several reasons: higher abundance of other pathogens, low viral titer, degraded nucleic acids, inadequate tissue lysis, low number of total reads, competition with host nucleic acids, etc. When sufficient reads are available, full or draft genomes will be reported.