Upload Genome FASTA

📝 Upload your genome sequence file in FASTA format. This will create a genome record that you can use for comparison.

Select CDS if your file contains coding sequences, or Genomic if you want Prokka to generate CDS first
Accepted formats: .fasta, .fa, .fna (Max: 200MB)
Upload to create a genome record

Select Species and Pan-Genome

🎯 Choose the species and pan-genome reference database for comparative analysis. Select a species first to see available pan-genomes.

Loading available species from database...

Run Comparison

🚀 Start the pan-genome comparison using your uploaded genome and selected pan-genome. This will compare your genome against the reference database and classify genes as core, accessory, or unique.

Optional Processing Steps
Select Chart Types
Compare uploaded genome with selected pan-genome

Check Tool Installation

Verify that Prokka and eggnog-mapper are installed and accessible.

Compare Annotation Tools

Upload a FASTA file to compare Prokka and eggnog-mapper performance and results.

Upload a genome sequence file to annotate with both tools
Prokka

Rapid prokaryotic genome annotation tool. Fast and reliable for bacterial genomes.

  • Speed: Very fast (~2-5 minutes)
  • Focus: Gene finding & basic annotation
  • Output: GFF, GenBank, protein files
Installation: conda install -c bioconda prokka
eggNOG-mapper

Functional annotation based on orthology. Provides COG categories and GO terms.

  • Speed: Slower (~20-90 minutes)
  • Focus: Detailed functional annotation
  • Output: Excel, TSV with COG/GO data
Installation: conda install -c bioconda eggnog-mapper
FastANI

Fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). Compares genomes to determine similarity.

  • Speed: Fast (~1-10 minutes)
  • Focus: Genome similarity & ANI calculation
  • Output: ANI values, alignment statistics
Installation: conda install -c bioconda fastani docker pull staphb/fastani:latest

Task Monitor

Monitor real-time task execution, worker status, and detailed job analytics.

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