Computational protocol: BA71ΔCD2: a New Recombinant Live Attenuated African Swine Fever Virus with Cross-Protective Capabilities

Similar protocols

Protocol publication

[…] Viral genomic DNA was extracted from semipurified BA71ΔCD2 preparations using the Nucleospin viral RNA and DNA isolation kit according to the manufacturer's instructions (Macherey-Nagel) and sent to Servei de Genomica from the Universitat Autònoma de Barcelona for Illumina paired-end 2 × 250-bp sequencing according to the manufacturer's instructions (MS-102-2003 MiSeq reagent kit v2; 500 cycles). Read pairs were quality checked and joined using fastqjoin software (). De novo assembly was done using A5 assembler pipeline () under the default parameters, and the scaffold_builder tool () was used for scaffolding the contigs. The assembled genome was compared with that of the ASFV parental virulent BA71 strain (GenBank accession number KP055815.1) () using Artemis Comparison Tool (), and Gepard software 1.4v was used to calculate dot plots for genome comparisons (). The BA71 sequence (GenBank accession number KP055815.1) was also used as the reference to perform the mapping of the joint reads with bwa (), using the mem algorithm. Samtools utilities () were used for calculating coverage, for single nucleotide polymorphism (SNP) calling, and to further process files for manual inspection using the Integrative Genomic Viewer (, ). […]

Pipeline specifications

Software tools scaffold_builder, ACT, Gepard, BWA, SAMtools
Applications De novo sequencing analysis, Genome data visualization
Organisms Sus scrofa