Genomic Analysis Tools

These genomic analysis tools support species identification, strain typing, antimicrobial resistance detection, and comparison of closely related bacterial genomes. Together, they enable users to analyze sequencing data for research, surveillance, and outbreak investigation purposes.

• KmerFinder

  KmerFinder allows users to quickly identify the bacterial species in sequence data. After uploading the sequencing file(s),
  KmerFinder compares them to reference databases to determine which species the sample belongs to. Users can upload a single Fasta file or one/two Fastq files.

• MLST

  This tool is for performing Multilocus Sequence Typing (MLST) to place bacteria into internationally recognized sequence types, supporting comparison across studies and labs. Users can upload a single Fasta file or one/two Fastq files.

• ResFinder

  ResFinder scans sequence data to identify known resistance genes and point mutations that may affect antimicrobial susceptibility. Users can upload a single Fasta file or one/two Fastq files.

• MINTyper

  This tool compares closely related samples using single-nucleotide polymorphism (SNP) analysis on Oxford Nanopore Technology (ONT) data. Users can upload a reference file as a Fasta file (optional), and upload at least two closely related Fastq files as their input.

• CSI Phylogeny

  This tool compares closely related samples using single-nucleotide polymorphism (SNP) analysis on Illumina data. Users can upload a reference file as a Fasta file, and upload at least two closely related Fasta or Fastq files as their input.