dbjohnson / d3igv

Hobby project using D3 to create a lightweight genomic sequencing data viewer

d3igv

This is a hobby project using D3 to recreate a lightweight Integrated Genome Viewer-like interface for viewing genomic sequencing data.

A sample BAM file is included, along with a crude model that can be used to generate simulated reads. The bedfile for the sample BAM was generated using the make_bedfile.py script, which simply searches for regions with good coverage.

Quickstart

Task	Command
Dependencies	pip install -r requirements.txt
HTTP server	gunicorn app:wsgi

Sample output

Live demo

API Routes

POST /reads

{
  "chrom": "chr1",
  "start": 10000,
  "end": 10100
}

Sample output

{
  "reference": "TGCTAGCTGG",
  "coverage": [
    {
      "A": 0,
      "C": 0,
      "G": 1,
      "T": 13,
    },
    {
      "A": 0,
      "C": 0,
      "G": 7,
      "T": 0,
    },
    ...
  ],
  "reads": [
    {
      "fwd": false,
      "start": 4,
      "sequence": "AGCT"
    },
    {
      "fwd": true,
      "start": 2,
      "sequence": "CTAGC"
    },
    ...
  ]
}