Quick Start

Annotate an Assembled Genome

This is the fastest way to use PIPA — upload an assembled genome and run annotation tools.

Via Web UI

1. Open http://localhost:8080
2. Click Start to go to the Software page
3. Select Annotation Only workflow
4. Upload your FASTA file (.fasta, .fa, or .fna)
5. Select annotation tools (Prokka, MLST, Barrnap, Abricate are on by default)
6. Set the genus and species of your organism
7. Click Submit
8. Monitor progress on the Results page

Via API

# Upload a FASTA file
curl -X POST http://localhost:5000/api/upload \
  -F "illumina=@my_assembly.fasta"

# Start annotation (replace JOB_ID with the returned job_id)
curl -X POST http://localhost:5000/api/run \
  -H "Content-Type: application/json" \
  -d '{
    "job_id": "JOB_ID",
    "genus": "Escherichia",
    "species": "coli",
    "input_type": "assembly",
    "tools": ["prokka", "mlst", "barrnap", "abricate"]
  }'

# Check status
curl http://localhost:5000/api/status/JOB_ID

# Get results when complete
curl http://localhost:5000/api/results/JOB_ID

Run the Full Pipeline

For raw sequencing reads (FASTQ), PIPA runs trimming, assembly, then annotation.

Via Web UI

1. Select Full Pipeline (Raw Reads) workflow
2. Check Illumina, Nanopore, or PacBio
3. Upload your FASTQ files (paired-end or single-end)
4. Set genome size (for Nanopore/PacBio assembly)
5. Click Submit

Via API

# Upload paired-end Illumina reads
curl -X POST http://localhost:5000/api/upload \
  -F "illumina=@reads_R1.fastq.gz" \
  -F "illumina=@reads_R2.fastq.gz" \
  -F "illumina_type=paired"

# Start full pipeline
curl -X POST http://localhost:5000/api/run \
  -H "Content-Type: application/json" \
  -d '{
    "job_id": "JOB_ID",
    "genus": "Klebsiella",
    "species": "pneumoniae",
    "input_type": "reads",
    "genome_size": "5.5m"
  }'

Example with Test Data

bash examples/run_example.sh