The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

van Rijn, Anneloes L.; van Boheemen, Sander; Sidorov, Igor; Carbo, Ellen C.; Pappas, Nikos; Mei, Hailiang; Feltkamp, Mariet; Aanerud, Marianne; Bakke, Per; Claas, Eric C. J.; Eagan, Tomas M.; Hiemstra, Pieter S.; Kroes, Aloys C. M.; de Vries, Jutte J. C.

For samples with dubious or inconclusive classification results a de novo assembly was performed. Pre-processed short reads assigned to a higher taxonomic level of a suspected viral target were extracted and de novo assembled with SPAdes version 3.11.1 [23] into longer stretches of contiguous sequences (contigs). The resulting contigs were then run against the blast NCBI's nucleotide (nt) database (accessed 2017) using blastn 2.7.1 [24] . After identification of a putative target sequence, all the reads from the original sample were mapped against the identified best BLAST hit for further confirmation using BWA 0.7.17 software package [25] .