Bioinformatician

This is a fully remote position, open to applicants in United States.

📋 Description

• Design, implement, sustain, and enhance bioinformatics workflows.

• Conduct quality control, assembly, annotation, and analysis of environmental metagenomic sequencing data.

• Analyze whole genome sequencing and metagenomic datasets utilizing established computational techniques.

• Develop statistical methods to detect variants and estimate pathogen abundance from sequencing datasets.

• Generate standardized bioinformatics outputs for integration into surveillance systems.

• Assist in the validation and testing of bioinformatics workflows and analytical pipelines.

• Manage high-throughput sequencing raw and processed data, databases, and uploads to sequencing repositories.

• Provide support for cloud-based and high-performance computing environments utilized for bioinformatics analyses.

• Implement quality assurance and quality control measures throughout bioinformatics workflows.

• Execute wastewater and environmental metagenomic pipelines, covering preprocessing, taxonomic classification, and abundance estimation.

• Maintain curated reference databases for environmental metagenomics.

• Assist in waterborne and environmental outbreak responses by processing and analyzing outbreak sequencing data.

• Conduct metagenomic source attribution analyses and prepare summary outputs.

• Perform in silico detection and characterization assays for environmental NGS datasets.

• Conduct quality control, reference-based assembly, variant calling, and annotation for viral whole genome sequencing.

• Support phylogenetic analyses of viral genomes and produce trees and summary statistics.

• Operate and monitor Nextflow pipelines in HPC and cloud settings; troubleshoot errors and document solutions.

• Develop and refine components of pipelines, modular scripts, and workflow steps.

• Manage sequencing data and analytic files, including uploads to NCBI and other repositories.

• Write and maintain Python, R, and Bash scripts within Linux environments.

• Execute database queries and routine data management across PostgreSQL, MySQL, and MongoDB.

• Maintain code using Git/GitHub/GitLab and adhere to documentation standards.

• Prepare reports and presentations summarizing sequencing results and quality metrics.

• Develop and update standard operating procedures for bioinformatics.

• Assist in manuscript preparation and data submission for journals and conferences.

• Assess bioinformatics software using benchmarks and performance metrics, synthesize findings, and recommend tools.

• Keep abreast of scientific literature for emerging bioinformatics methodologies and software.

⛳️ Requirements

• A minimum of 2-5 years of relevant experience.

• Experience in implementing and maintaining bioinformatics pipelines.

• Familiarity with sequencing data and genomic analyses.

• Strong Python programming skills, particularly in bioinformatics data analysis.

• Experience in creating visualizations using Python or R (ggplot2).

• Proficient in using Git-based version control systems.

• Knowledge of database design principles and data management.

• Capability to troubleshoot analytical workflows and resolve computational challenges.

• Ability to work independently while effectively collaborating within multidisciplinary teams.

• Proficient in Python, R, and Bash in Linux/HPC environments.

• Working experience with Nextflow; familiarity with Snakemake or similar workflow managers is a plus.

• Experience with Docker and Singularity.

• Familiarity with Bowtie2, SPAdes, minimap2, prokka/bakta, and other open-source bioinformatics tools.

• Understanding of Git, GitHub, and GitLab.

• Familiarity with NCBI data submission standards and cloud computing environments.

• Experience supporting federal government programs, preferably with the CDC, is preferred.

🏝️ Benefits

• Medical insurance.

• Dental insurance.

• Vision insurance.

• 401(k) plan with company matching.

• Tax-deferred savings options.

• Supplementary benefits.

• Paid time off.

• Opportunities for professional development.