Build a Research Cohort Genomic Assay Quality Indexer

Aggregate sequencing quality parameters from multi-sample FASTA archives and index metrics into search records. Generate FHIR DiagnosticReport entities to support observational research cohort discovery.

Bioinformatics Platform Engineer

Parse multi-sample FASTA sequence files and extract per-sequence base composition statistics.

Compute GC-content percentages and ambiguous N-base ratios using Biopython.

Index computed quality records with metadata tags into a local vector and document index.

Compile batch quality metrics into FHIR DiagnosticReport bundles for registry integration.

REST API endpoint paired with a web table displaying GC% distributions, N-base ratios, and bundle download links.

Assemble public FASTA test files via NCBI Datasets command for human mitochondrial or bacterial genes. Starter examples below are synthetic. They are not downloaded records.

Biopython Employs Biopython's Bio.SeqUtils module to parse FASTA files and quantify GC content.

llamaindex, biopython, chromadb. llamaindex indexes structured bioinformatics quality metrics and allows natural-language semantic cohort querying. Hosted or local embedding model for index construction; API-based LLM for cohort query answering.

Submit runnable source, pinned dependencies, setup commands, a working interface, example outputs, and a recorded end-to-end demo. Include tests and an action log.

Calculate GC content percentage within 0.1% accuracy for each sequence.

Construct valid FHIR DiagnosticReport resources linking sample quality metrics.

Index at least 50 sample records and verify semantic lookup by quality criteria.

```json [ { "input": { "sample_id": "COHORT_S1", "fasta_sequence": "ATGCGATCGATCGATC" }, "expected_output": { "sample_id": "COHORT_S1", "gc_percent": 50, "n_ratio": 0, "quality_flag": "PASS", "fhir_report": { "resourceType": "DiagnosticReport", "status": "final" } } }, { "input": { "sample_id": "COHORT_S2", "fasta_sequence": "NNNATGCNNNNNGATC" }, "expected_output": { "sample_id": "COHORT_S2", "gc_percent": 25, "n_ratio": 0.5, "quality_flag": "REJECT", "fhir_report": { "resourceType": "DiagnosticReport", "status": "preliminary" } } } ] ```

Research data platform indexing sequence assay metrics without patient identity or health advice. Use mock external writes. Require human review before any real deployment.