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.
Task | Command |
---|---|
Dependencies | pip install -r requirements.txt |
HTTP server | gunicorn app:wsgi |
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"
},
...
]
}