Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine

Table 1 Concise overview of each step in the sequencing data processing workflow

Step	Key Tools	Link
Quality Control	FastQC, MultiQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://multiqc.info/
Read Trimming and Filtering	Trimmomatic, Cutadapt	http://www.usadellab.org/cms/?page=trimmomatic https://cutadapt.readthedocs.io/en/stable/
Read Alignment/Mapping	BWA, Bowtie2, STAR, Minimap2	https://bio-bwa.sourceforge.net/ https://bowtie-bio.sourceforge.net/bowtie2/index.shtml http://code.google.com/p/rna-star/. https://github.com/lh3/minimap2
Variant Calling	GATK, FreeBayes, Samtools	https://gatk.broadinstitute.org/hc/en-us https://github.com/freebayes/freebayes http://samtools.sourceforge.net
Annotation	ANNOVAR, SnpEff, VEP	http://www.openbioinformatics.org/annovar/. https://pcingola.github.io/SnpEff/ https://www.ensembl.org/info/docs/tools/vep/index.html
Data Visualization	IGV, UCSC Genome Browser	https://igv.org/ https://genome.ucsc.edu/

ISSN: 1743-422X