Senior Bioinformatics Programmer
$84,578–$105,040 year
On-siteNew York, United States
Job Summary
Develop automated workflows and pipelines within a Nextflow environment for clinical diagnostic assays using next-generation sequencing data. Analyze molecular patient data from the clinical lab, perform quality control on sequencing data, and develop solutions to enhance future performance. Oversee systems support for existing pipelines and create new ones to support molecular assays, while independently analyzing genomics-based approaches. Collaborate with clinicians, scientists, and pathologists to interpret patient NGS results for treatment options and address clinical needs using bioinformatics techniques. Work with the MCIIT and HPC team to provide server and storage solutions. Perform multi-omics data analysis and integration, utilizing Python, R, shell scripting, and Nextflow to manipulate FASTQ, BAM, and VCF files.
Required Qualifications
- M.Sc. degree
- Minimum of 3 years' experience in Bioinformatics, Computer Science, Programming, Software Development, or related field
- Previous experience with NGS data and associated bioinformatics tools
- Experience in Unix/Linux systems including high-performance computing environments
- Strong programming skills in Python, R, shell scripting
- Proficiency in Nextflow, Django, Docker and Singularity containers
- Work experience and algorithm understanding of standard software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools
- Knowledge in the analysis of SNV, Indel, CNV and structural variants for both somatic and germline disease, additional understanding of variant annotation
- Familiarity with various NGS QC principles
- Knowledge of biology, cancer genomics or an understanding of key and complex biological concepts
- Detail-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics
- Ability to work independently (e.g., recommend new software or bioinformatic tools, find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results)
- Team oriented with excellent written and verbal communication skills
- Ability to function in a multidisciplinary team including MD's and PhD's
- Ability to effectively communicate with all levels of the organization
- Ability to be onsite 3 to 5 days a week
- Possibility of full remote work is currently not available
Desired Qualifications
- Expert in creating customized sequencing analysis pipelines, in applications for data analysis, and executing standard bioinformatics pipelines (relevant examples in a GitHub repository)
- Basic knowledge and understanding of software engineering concepts
- Knowledge of algorithms, data structures, machine learning
- Prior experience working in CLIA environment is a plus
- Experience in variant calling benchmarking and clinical validation analysis (e.g. concordance, limit of detection, assay reproducibility)
- Experience with running workflows on public cloud (GCP / AWS)
- Experience with developing and querying databases using SQL queries
- Experience with web-development (HTML, CSS, JavaScript, TypeScript and related)
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