Build a Research Molecular Assay Quality Indexer and Haystack Search Engine

Aggregate sequencing quality scores and coverage metrics from FASTA batches. Index quality metrics into Haystack document stores to assist observational study cohort selection.

Genomics Core Facility Manager

Parse multi-sample FASTA archives to compute sequence length distributions and GC content percentages.

Aggregate run-level quality control indicators across research specimen batches.

Index structured assay quality documents into a Haystack in-memory or OpenSearch document store.

Query assay cohorts using conversational parameters and export filtered FHIR DiagnosticReport bundles.

React web application with cohort filter sliders, interactive GC-content histograms, and search query box.

Construct mock high-throughput sequencing run archives containing synthetic FASTA files with varied lengths and base distributions. Starter examples below are synthetic. They are not downloaded records.

Biopython Uses Biopython SeqIO to parse multi-record FASTA files and compute sequence composition properties.

haystack, biopython, pydantic. Haystack coordinates document store indexing, hybrid metadata filtering, and semantic query pipelines. Local or hosted LLM to interpret complex natural language criteria for research cohort retrieval.

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.

Calculates GC content and sequence length metrics for all FASTA entries using Biopython.

Populates Haystack Document Store with metadata attributes for rapid cohort filtering.

Returns valid search results matching specified GC content and quality threshold filters.

```json [ { "input": { "batch_id": "RUN_001", "fasta_content": ">seq1\nATGCGATCGA\n>seq2\nGCGCGCGCGC\n" }, "expected_output": { "total_sequences": 2, "mean_gc_content": 0.75, "indexed": true, "eligible_for_high_gc_cohort": true } }, { "input": { "batch_id": "RUN_002", "fasta_content": ">seq_empty\n\n" }, "expected_output": { "total_sequences": 0, "mean_gc_content": 0, "indexed": false, "error": "Empty FASTA records detected in batch RUN_002" } } ] ```

Research assay quality metrics only; contains no protected patient identifiers or clinical diagnoses. Use mock external writes. Require human review before any real deployment.