Salmonella whole genome sequence analysis of 300bp pair end reads.
All the code used in "Genomic Diversity, Antimicrobial Resistance, Plasmidome, and Virulence Profiles of Salmonella Isolated from Small Specialty Crop Farms Revealed by Whole-Genome Sequencing" "https://www.mdpi.com/2079-6382/12/11/1637" manuscript to analyze the datasets and create the figure is available in this repository:
- Fastqc - Quality of seqeunces
- Multiqc - View the results collectively
- Trimmomatic - Trim the adapters and primers
- SPADES - Genome assembly
- PROKKA - Annotation of genome
- Roary - Pan genome analysis
- SeqSero2 and MLST - Serotyping and seqeunce typing
- kSNP3 - SNPs identification
- AMRFinderPlus - Antimicrobial resistance genes
- ABRicate - Virulence genes
- MOB-suite - Plasmids