Hiseq x lane

We obtained a sample of N. phaeopus (ZMUC 112728) from the Natural History Museum of Denmark, Copenhagen, for reference genome assembly. Its genomic DNA was extracted using the KingFisher Duo Prime Magnetic Particle Processor (Thermo Fisher Scientific, USA) and the KingFisher Cell and Tissue DNA Kit (Thermo Fisher Scientific). A linked-read sequencing library was prepared using the Chromium Genome library kits (10 X Genomics) and sequenced on one Illumina Hiseq X lane at SciLifeLab Stockholm (Sweden). The de novo assembly analysis was performed using 10 X Chromium Supernova (v. 2.1.1). Reads were filtered for low quality and duplication, while assemblies were checked for accuracy and coverage and the best assembly was selected based on the highest genome coverage with the fewest errors. The final genome had a size of 1.12 Gb at a coverage of 50 X with N50=3504.2 kbp.

Detailed laboratory and bioinformatic procedures for the following are provided in Supplemental Material 2. 1) Three pools were prepared, with each pool containing one replicate library from each AIV isolate. These pools were sequenced in-house on Illumina MiSeq to generate full HA, NA, and M segment sequences for each isolate and to confirm HA and NA subtypes. 2) Each pool was diluted in 1:100 (ng/ng) in one of three replicate libraries of background genomic material that had been prepared from a mock-infected chicken egg. Aliquots of each diluted pool were sequenced pre-capture at Canada’s Michael Smith Genome Sciences Centre (Vancouver, BC) on one Illumina HiSeq X lane to establish baseline HA, NA, and M segment abundance. 3) Each diluted pool was independently captured using the AIV_v1 probe panel. Captured pools were then sequenced in-house on Illumina MiSeq to assess target enrichment of HA, NA, and M segments post-capture.