Build Clinical Bioinformatics Pipeline
Budget: ₹75,000 – ₹150,000 INR
**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.
**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.