ASFV-989 Strain Genome Sequencing

DNA was extracted from the ASFV-989 strain with the High Pure PCR Template Preparation Kit (Roche Diagnostics, Meylan, France). For library preparation, the Ion Xpress Plus Fragment Library Kit and the Ion Xpress Barcode Adapters 1–96 Kit (Thermo Fisher Scientific, Frederick, MD, USA) were used, and barcoded DNA fragments between 250 bp and 290 bp were size-selected with magnetic beads from the Agencourt AMPure XP Kit (Beckman Coulter, Villepinte, France). All samples were sequenced with the Proton Ion Torrent technology (Thermo Fisher Scientific, Frederick, MD, USA). The raw reads were cleaned with the Trimmomatic [38 (link)] 0.36 software (ILLUMINACLIP: oligos.fasta: 2:30:5:1: true; LEADING: 3; TRAILING: 3; MAXINFO: 40:0.2; MINLEN: 36). Then, a bwa [39 (link)] (version 2.2.5) alignment was performed with cleaned reads versus NCBI reference FR682468.2. The consensus sequence was created with SAMtools [40 (link)] (version 1.8) and seqtk (version 1.2) (https://github.com/lh3/seqtk accessed on 17 July 2016). The obtained sequence was annotated with Prokka (Galaxy version 1.13), and then compared to the Georgia 2007/1 strain sequence [NC_044959.1] using Seaview (version 5.0) and the seg.sites {ape} function in R 3.6.1.
Data availability: all sequence data were uploaded to the NCBI under the study accession number PRJNA784367.