📊 Assembly Statistics Calculator

Calculate comprehensive assembly statistics including N50, L50, GC content, scaffold count, total length, and more. Essential for genome assembly quality assessment and comparative analysis.

Input Method:

⚙️ Analysis Parameters

Ignore scaffolds shorter than this length

📈 Assembly Statistics Results

-
Total Length (bp)
-
Scaffold Count
-
N50 (bp)
-
L50
-
GC Content (%)
-
Execution Time (s)

📋 Detailed Assembly Metrics

Metric Value Description

🔧 Command-Line API Usage

You can use the stats API directly from the command line with curl:

Basic Usage:

curl -X POST https://bbmapservers.jgi.doe.gov/stats/api/stats \
  -H "Content-Type: application/json" \
  -d '{"sequence": ">scaffold1\nATCGATCG\n>scaffold2\nGCTAGCTA"}'

With a FASTA File:

# Method 1: Read file into JSON
curl -X POST https://bbmapservers.jgi.doe.gov/stats/api/stats \
  -H "Content-Type: application/json" \
  -d "{\"sequence\": \"$(cat contigs.fa)\"}"

# Method 2: Use jq for proper JSON escaping
curl -X POST https://bbmapservers.jgi.doe.gov/stats/api/stats \
  -H "Content-Type: application/json" \
  -d "$(jq -n --arg seq "$(cat contigs.fa)" '{sequence: $seq}')"

Response Format:

{
  "success": true,
  "execution_time": 126,
  "statistics": {
    "scaffolds": 2,
    "scaf_bp": 16,
    "scaf_N50": 1,
    "scaf_L50": 8,
    "gc_avg": 50.0,
    ...
  }
}

Note: The API accepts FASTA format sequences and returns detailed assembly statistics in JSON format.