**Job Title:** Bioinformatics Consultant – LP-WGS (Reproductive Genomics) **Location:** Remote (India preferred) **Engagement Type:** Contract / Freelance (3–6 months, extendable) **Start Date:** Immediate --- ## **About the Project** We are setting up a **clinical-grade bioinformatics pipeline** for **low-pass whole genome sequencing (LP-WGS)** focused on reproductive genomics applications including: * Non-Invasive Prenatal Testing (NIPT) * Products of Conception (POC) analysis * Recurrent Pregnancy Loss (RPL) analysis The pipeline must be **robust, reproducible, and compliant with clinical lab standards (NABL/ISO 15189)**. --- ## **Scope of Work** You will design, develop, and validate an end-to-end bioinformatics pipeline for LP-WGS data. ### **Key Responsibilities** * Develop a **scalable LP-WGS pipeline** from FASTQ → CNV calls → report-ready outputs * Implement alignment, QC, normalization, and CNV calling workflows * Integrate tools such as BWA, CNVkit, Control-FREEC, and WISECONDORX * Implement **GC bias correction, binning, and segmentation algorithms** * Develop modules for: * Aneuploidy detection (NIPT) * CNV detection (POC/RPL) * LOH and maternal contamination assessment * Optimize pipeline for **low-coverage sequencing (0.1×–1×)** * Create **automated QC metrics and flags** * Ensure reproducibility using workflow managers (Snakemake/Nextflow) * Containerize pipeline (Docker preferred) * Generate clear documentation (user manual + technical SOP) --- ## **Deliverables** * Fully functional pipeline (CLI-based) * Test dataset results + validation report * QC dashboard/reporting templates * Installation & deployment guide * Code repository with version control --- ## **Required Skills & Experience** ### **Must Have** * 3+ years in **bioinformatics / NGS data analysis** * Proven experience with **low-pass WGS or CNV analysis** * Strong hands-on experience with: * BWA, SAMtools * CNVkit, Control-FREEC * Experience working with **human genome data (hg19/hg38)** * Proficiency in Python / R / Bash * Experience with Linux-based environments --- ### **Good to Have (Highly Preferred)** * Experience with **NIPT / cfDNA analysis** (WISECONDORX or similar) * Experience in **clinical genomics pipelines** * Knowledge of **fetal fraction estimation methods** * Experience with **LOH, mosaicism, or contamination detection** * Familiarity with **NABL / CAP / CLIA requirements** * Experience with workflow tools (Snakemake / Nextflow) * Docker / containerization experience --- ## **Selection Process** * Resume + project portfolio review * Short technical discussion * **Paid test assignment** (real LP-WGS dataset) --- ## **What We’re Looking For** * Someone who has **built real pipelines**, not just analyzed data * Strong understanding of **low-depth sequencing challenges** * Ability to translate bioinformatics into **clinical-grade outputs** * Clear communicator with documentation discipline --- ## **Compensation** * Competitive, based on experience and deliverables * Milestone-based payments --- ## **How to Apply** Please share: * Updated CV * Links to GitHub / past work (if available) * Brief description of relevant LP-WGS / CNV projects --- **Note:** Candidates with prior experience in **reproductive genomics or clinical diagnostics** will be strongly preferred.