Introduction

This R Markdown demonstrates the usage of AMRScan.R to identify antimicrobial resistance genes from a FASTQ file.

Load Script

source("scripts/AMRScan.R")
## Detected FASTA input. Skipping quality filtering.
## BLAST database already exists. Skipping makeblastdb.
## Running BLASTX on input FASTA: data/GCF_037966445.1_ASM3796644v1_genomic.fna 
## AMRScan completed. Results saved to: results/

Results

summary_file <- "results/final/GCF_037966445.1_ASM3796644v1_genomic_AMR_hits_summary.csv"
if (file.exists(summary_file)) {
  amr_summary <- read.csv(summary_file)
  knitr::kable(head(amr_summary), caption = "Top AMR Hits Summary")
} else {
  cat("Summary file not found.")
}
Top AMR Hits Summary
Query Subject Identity Length Evalue Bitscore Annotation
NZ_JBBPBW010000028.1 gb|BAM10414.1|ARO:3003039|OprA 40.839 453 0 252 gb|BAM10414.1|ARO:3003039|OprA [Pseudomonas aeruginosa]
NZ_JBBPBW010000035.1 gb|ABV89601.1|ARO:3004826|LAP-2 100.000 285 0 587 gb|ABV89601.1|ARO:3004826|LAP-2 [Enterobacter cloacae]
NZ_JBBPBW010000001.1 gb|CAA66729.1|ARO:3001070|SHV-11 100.000 286 0 581 gb|CAA66729.1|ARO:3001070|SHV-11 [Klebsiella pneumoniae]
NZ_JBBPBW010000010.1 gb|CCI79240.1|ARO:3005047|eptB 99.303 574 0 1109 gb|CCI79240.1|ARO:3005047|eptB [Klebsiella pneumoniae subsp. rhinoscleromatis SB3432]
NZ_JBBPBW010000104.1 gb|AHK10285.1|ARO:3002859|dfrA14 98.726 157 0 327 gb|AHK10285.1|ARO:3002859|dfrA14 [Escherichia coli]
NZ_JBBPBW010000011.1 gb|AAC75271.1|ARO:3003952|YojI 83.912 547 0 885 gb|AAC75271.1|ARO:3003952|YojI [Escherichia coli str. K-12 substr. MG1655]