About Genome Comparator

Genome Comparator compares genome assemblies against loci extracted from an annotated reference genome.

It uses BLASTN to find qualifying locus matches, infers allele indices during the run, and reports allele profiles, variable loci, core loci, paralogues, and pairwise distances.

Prefer to run Genome Comparator locally or from a pipeline? Get the standalone Python command-line tool on GitHub .

See an example output here.

  • Genome Comparator: 0.1.0
  • Python: 3.12
  • NCBI BLAST+: 2.17.0
  • Biopython: 1.83
  • Flask: 3.0.3
  • Gunicorn: 23.0.0
  • gevent: 24.11.1
  • RQ: 2.1.0
  • redis-py: 5.2.1

Submit your job

STEP 1: Upload an annotated reference genome

STEP 2: Upload one or more genome FASTA files, gzip-compressed FASTA files, or a ZIP/TAR archive

N.B. Multiple FASTA files can be selected together. Gzip-compressed FASTA and ZIP/TAR archives are checked before a job is created; unsupported, corrupt, or invalid inputs are rejected.

Drag and drop FASTA files, gzip-compressed FASTA files, or a ZIP/TAR archive here, or click to select

STEP 3: Select your comparison parameters

STEP 4: Clear or hit Submit

Contact us

For queries and to report any issues, email us at: email[at]biology.ox.ac.uk

Ineos Oxford Institute for antimicrobial research

University of Oxford

Sir William Dunn School of Pathology

South Parks Road

Oxford, OX1 3RE

United Kingdom

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