- - VA-Charlottesville
- Charlottesville, VA, USA
- Part Time
This is a part-time (maximum of 29hrs / week ) internship position for the Summer months (~May – August. The individual will functionally report to a member of the HS Bioinformatics team and will assist with MinION pipeline development. An area of frequent complaint and potential significant improvement in nanopore-based sequencing (e.g. Oxford Nanopore MinION) is that the data analysis requires a significant level of bioinformatics expertise. Creation of a streamlined pipeline for analysis of forensic SNP genotyping data from raw MinION reads would enable analysts to reproducibly and easily access this kind of data without requiring advanced bioinformatics training. Ideally, the pipeline would include all steps from basecalling and quality control through final profile creation, run in a workflow manager like Snakemake or NextFlow, and be containerized through Docker or singularity. The individual in this role will build on existing SigSci R&D, building and testing a pipeline with the eventual goal of creating a workflow that would be both publishable and relevant to SigSci future work.
Essential Duties and Responsibilities:
- Develop containerized pipeline for analysis and SNP genotyping from MinION (or other) sequencing data.
- Develop tools for management, analysis and interpretation of other high-density microarray and whole genome sequencing data.
- Managing, manipulating, analyzing data using a combination of R, python, and UNIX tools.
- Using established domain-specific open-source software and tools to manipulate and analyze genomic data.
- Implement and execute data processing workflows and automated analytic pipelines.
- Create standardized summary tables and figures using literate programming and reproducible workflows.
- Conduct workflow benchmarking and documentation, identifying inconsistencies and resolving data problems.
Required Knowledge, Skills & Abilities (KSA's):
- Proficiency working in a Unix/Linux environment.
- Proficiency with R, RMarkdown, and the "tidyverse" tools for data analysis.
- Proficiency with open-source software, tools, and databases for analyzing next-generation sequencing data (whole-genome sequencing, RNA-seq, epigenetics, microbiome, and/or metagenomics).
- Experience or willingness to gain experience with NextFlow, SnakeMake, or similar workflow/pipeline management systems.
- Familiarity using git and GitHub for version control and collaboration is desired.
- Familiarity with Docker and/or Singularity is desired.
Education/Experience: Current enrollment in a genomics, bioinformatics, computational biology, or similar MS or PhD program, with an emphasis on scientific computing (either through coursework or mentored laboratory research).
Certificates and Licenses: None.
Citizenship: United States.
Clearance: Ability to obtain a DOD Clearance.
Supervisory Responsibilities: N/A.
Working Conditions/ Equipment: Ability to work in varying conditions to include: traditional office environments with sedentary extended periods required for code development and testing.
- Most current college and/or university transcript(s).
- GitHub profile, if available.