Endangered wild salmon infected by newly discovered viruses

Mordecai, Gideon J; Miller, Kristina M; Di Cicco, Emiliano; Schulze, Angela D; Kaukinen, Karia H; Ming, Tobi J; Li, Shaorong; Tabata, Amy; Teffer, Amy; Patterson, David A; Ferguson, Hugh W; Suttle, Curtis A

The quality of the raw reads was checked using FASTQC (v0.11.7) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality reads or regions of adapter sequences were removed using Trimmomatic (v0.36) (Bankevich et al., 2012) . Reads were aligned to the Atlantic Salmon genome using bwa mem (v0.7.17-r1188) and unmapped reads were retained. The unmapped reads were then balanced using Trimmomatic and assembled into contigs using SPAdes (v3.9.1) genome assembler (Bankevich et al., 2012) . Putative viral contigs were identified by aligning translated contigs using DIAMOND (v0.9.16.117) (Buchfink et al., 2015) to the nr database. Reference alignments of all the reads to the viral contigs were used to ensure that no assembly artefacts occurred and the contigs were trimmed appropriately using Geneious (V10.1.3). Assembled sequences are available on Genbank (BioProject: PRJNA547678, Genbank accession numbers: MK611979 -MK611996) and raw sequencing reads have been uploaded to the Sequence Read Archive (SAMN11974798 -SAMN11974801).