Nasopharyngeal metagenomic deep sequencing data, Lancaster, UK, 2014-2015

Abstract

Nasopharyngeal swabs were taken from volunteers attending a general medical practice and a general hospital in Lancaster, UK, and at Lancaster University, in the winter of 2014-2015. 51 swabs were selected based on high RNA yield and allocated to deep sequencing pools as follows: patients with chronic obstructive pulmonary disease; asthmatics; adults with no respiratory symptoms; adults with feverish respiratory symptoms; adults with respiratory symptoms and presence of antibodies against influenza C; paediatric patients with respiratory symptoms (2 pools); adults with influenza C infection (2 pools), giving a total of 9 pools. Illumina sequencing was performed, with data yields per pool in the range of 345.6 megabases to 14 gigabases after removal of reads aligning to the human genome. The data were deposited in the Sequence Read Archive at NCBI, and constitute a resource for study of the viral, bacterial and fungal metagenome of the human nasopharynx in healthy and diseased states and comparison with other metagenomic studies on the human respiratory tract.

Figure 1. Clinical flowchart.

From 148 nasopharyngeal swabs, 51 were chosen for allocation to 7 symptom groups, of which 2 were divided into two separate runs, making a total of 9 deep sequencing pools.

Figure 2. Read processing flowchart.

The raw reads were cleaned and then subjected to sequential alignments to 3 versions of the human genome, with mapped reads discarded at each stage. The software used at each stage is shown.