Bioinformatics Specialist Job Listing at Rockefeller University in New York, NY (Job ID 1639)

Description

Organization Overview

Our Vertebrate Genome Laboratory conducts research and services for individual and large vertebrate genome projects such as the Vertebrate Genomes Project (VGP/G10K) that aims to sequence high-quality genomes for all 66,000 vertebrate species on the planet. https://vertebrategenomesproject.org/.
Overview

We seek a highly motivated individual with a strong background in Computer Science and Genomics to join the Bioinformatics team of the Vertebrate Genome Laboratory (www.vertebrategenomelab.org) at the Rockefeller University. This person will generate reference genomes of eukaryotic species as part of the Vertebrate Genomes Project (VGP, www.vertebrategenomesproject.org) and the Earth Biogenome Project (EBP, https://www.earthbiogenome.org/).

In particular, the individual is expected to help achieve the following goals:

• Work closely with the VGL data production and bioinformatics teams, and the broader international scientific community of the VGP, to actively generate draft high-quality genomes.
• Help make the current pipeline, which is already heavily streamlined, fully automated, such that the sequencing data is automatically processed into draft assemblies along with QC, ready for manual curation.
• Consistently improve the pipeline for genome assembly quality and efficiency, based on feedback from genome curators, incorporating novel data types, and adding or help in designing novel tools.

Our current workflow involves: 1) in-house generation of a variety of long- (PacBio, Nanopore) and short- (Hi-C, Element, Illumina) read data; 2) in-house generation of reference-grade draft genome assemblies; 3) manual curation of the draft assemblies; 4) submission of the final, curated assemblies to the public archives. The individual will be integrated in step 2, and will be responsible to run, maintain, further develop, and improve the VGL genome assembly pipeline currently implemented in Galaxy (Lariviere et al. 2024 Nature Biotechnology DOI: 10.1038/s41587-023-02100-3).

Responsibilities include:

• Genome assembly
• Genome assembly pipeline maintenance

The ideal candidate will have a sound knowledge of genomics, ideally with insights into genome assembly, genome curation and genome analysis.

Required:

• Master's degree required, Ph.D. preferred
• Educational emphasis in computer science or computational biology
• Strong programming skills, includin knowledge of computational data-analysis workflows (e.g. CWL)
• Familiarity with Unix and HPC environments
• The ability to work both independently and as part of a team

Preferred:

• Previous experience with Galaxy workflows is a plus
• The ability to organize, prioritize and plan a diverse range of work to meet deadlines
• An investigative and solution-orient mindset
• Good communication skills 
• Skilled in working effectively within large national and international scientific consortia

The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above.

The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting.

The ideal candidate will have a sound knowledge of genomics, ideally with insights into genome assembly, genome curation and genome analysis.

Required:

• Master's degree required, Ph.D. preferred
• Educational emphasis in computer science or computational biology
• Strong programming skills, includin knowledge of computational data-analysis workflows (e.g. CWL)
• Familiarity with Unix and HPC environments
• The ability to work both independently and as part of a team

Preferred:

• Previous experience with Galaxy workflows is a plus
• The ability to organize, prioritize and plan a diverse range of work to meet deadlines
• An investigative and solution-orient mindset
• Good communication skills 
• Skilled in working effectively within large national and international scientific consortia

The Rockefeller University does not discriminate in employment on the basis of race, color, religion, sex (including pregnancy, gender identity), national origin, political affiliation, sexual orientation, marital status, disability, genetic information, age, membership in an employee organization, retaliation, parental status, military service or other non-merit factor. All qualified applicants will receive consideration for employment without regard to the characteristics listed above.

The salary of the finalist selected for this role will be set based on various factors, including but not limited to organizational budgets, qualifications, experience, education, licenses, specialty, and training. The hiring range provided represents The Rockefeller University's good faith and reasonable estimate of the range of possible compensation at the time of posting.

Responsibilities include:

• Genome assembly
• Genome assembly pipeline maintenance