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README.md

stxtyper container

Main tool: stxtyper

Additional tools:

  • ncbi-blast+ 2.12.0

Basic information on how to use this tool:

  • executable: stxtyper
  • help: stxtyper --help
  • version: stxtyper --version
  • description: Detects and types Shiga toxin genes in nucleotide sequences

Full documentation: https://github.com/ncbi/stxtyper

Note: This software is now incorporated into NCBI's AMRFinderPlus software as of version 4.0.3. Stxtyper will run under-the-hood of AMRFinderPlus when using the amrfinder --organism Escherichia option.

Example Usage

# stxtyper accepts both gzipped and uncompressed FASTA files
stxtyper -n GCA_012224845.2_ASM1222484v2_genomic.fna.gz -o stxtyper-results.tsv

$ column -t test-result.tsv 
#target_contig  stx_type  operon    identity  target_start  target_stop  target_strand  A_reference  A_reference_subtype  A_identity  A_coverage  B_reference  B_reference_subtype  B_identity  B_coverage
CP113091.1      stx2o     COMPLETE  100.00    2085533       2086768      +              WAK52085.1   stxA2o               100.00      100.00      QZL10983.1   stxB2o               100.00      100.00