WGS of African Swine Fever Virus: Dominican Republic Swine (Illumina)
The best reference from the NCBI RefSeq database was determined by aligning reads against all references and selecting the reference genome with the closest identity and breadth of coverage.  The closest reference genome by identity was Georgia 2007/1 (NC_044959.2).  Reference-guided alignment was performed using BWA-MEM (0.7.17-r1188) for Illumina data and Minimap2 (version 2.21-r1071) for Oxford Nanopore data.  Variant calling against the Georgia 2007/1 reference was performed using Freebayes (version 1.3.4) against the population of samples.  Variants were filtered based on quality score, depth, and log-odds ratio to remove low-confidence variants.  This produced a sample set with 21 total variant sites, all of which were single nucleotide polymorphisms.  These variants were applied to the Georgia 2007/1 genome to produce the final consensuses.  Annotations were transferred from the Georgia 2007/1 genome, and changes in gene coding sequences were modified accordingly.  The samples in this BioProject include raw data files and genome consensus sequences against Georgia 2007/1 based on reference-guided assembly.