Bioinformatician – Pipeline Administrator & Developer

In the:
This role is to provide computational infrastructure support for the Bioinformatics Core (BABS) and the Advanced Sequencing Facility (ASF) at the Francis Crick Institute and will work jointly with members of both ASF and the Bioinformatics Core teams to achieve this. The ASF provides next generation sequencing capacity from multiple platforms to researchers across the Crick and requires computational support: to maintain and develop its Laboratory Information Management System (Clarity LIMS); to track sequence run metrics; to provide tools for the display and interrogation of these metrics; and to contribute to the development of pipelines with the Bioinformatics Core for automatically processing sequencing data. The role holder will report to the Heads of the ASF and the Bioinformatics Core.
Deadline for applications has passed.

Key information

Job reference
R910
Salary
Competitive
Applications closed
23 September 2022, 23:59 BST
Hours per week
36 (full time)
Contact
Email administrator
Posted 23 August 2022
Background texture taken from the lab imagery.

Bioinformatician – Pipeline administrator & developer – Bioinformatics & Biostatistics

Reports to: Head of Bioinformatics Core and Head of Advanced Sequencing Facility

This is a full-time, permanent position on Crick terms and conditions of employment.

         

Summary

The Francis Crick Institute seeks to recruit a collaborative
and self-motivated Bioinformatician to run and develop the Institute’s NGS data processing and analysis pipeline infrastructure. You will run, maintain and develop data processing pipelines using nf-core and Nextflow technologies for the Advanced Sequencing Facility, Pontus Skoglund’s Ancient DNA group and Bioinformatics team.

Project summary

In this role, you will maintain and develop the Nextflow NGS analysis pipeline infrastructure established by the Bioinformatics Core and Ancient DNA groups. A key responsibility will be to ensure all data generated by the Advanced Sequencing Facility is preprocessed and sequencing data made available for downstream analysis. You will also be responsible for running and developing specific analysis pipelines. You will work closely with Pontus Skoglund’s group, where you will be responsible for running, maintaining and developing the ancient DNA analysis pipelines that process sequencing data generated from these bespoke samples. You will also run and develop analysis pipelines across a wide range of sequencing applications within the Bioinformatics Core. In addition, the Crick is an active user and partner of nf-core and has contributed to several key nf-core pipelines (rnaseq, cutnrun, viralrecon & nanoseq). In this role, you will have the opportunity to continue to develop this relationship by supporting the use of nf-core within the Institute and developing pipeline development collaborations with the wider nf-core community.

Key responsibilities

  • Maintain the raw sequence data preprocessing pipelines, providing QC metrics and tools for performance analysis.
  • Manage the processing of sequencing data using nf-core and in-house analysis pipelines.
  • Develop new data processing pipelines for the latest NGS applications.
  • Maintain and develop the bespoke data processing pipelines used by the Ancient DNA research group.
  • Work closely with the sequencing team to ensure QC standards are met.
  • Work closely with analysts in the bioinformatics team to ensure processed results are suitable for downstream analysis.
  • Help to develop methods for delivering results to Crick scientists.
  • Support nf-core and Nextflow efforts within the Crick.
  • Interact with the wider nf-core/Nexflow community.

Key experience and competencies

The post holder should embody and demonstrate our core Crick values: bold, imaginative, open, dynamic and collegial, in addition to the following:

Essential

  • A degree in a relevant subject with an extensive analytical component, e.g. bioinformatics, statistics, molecular biology or mathematics.
  • Experience in applying bioinformatics to project work in a collaborative biological research environment.
  • Excellent scientific analysis skills.
  • Demonstrable programming experience in Nextflow.
  • Familiarity with software design patterns and technologies used to ensure analysis reproducibility such as nf-core best practice and containerisation.
  • Experience in software development processes and management using GitHub
  • Experience in processing NGS data using a variety of bioinformatics analysis software.
  • Experience in running bioinformatics analysis software on an HPC Linux system.
  • Familiarity with NGS analysis methodologies and protocols.
  • The ability to work independently on tasks and organise and prioritise workload within a project management framework.
  • Excellent scientific communication skills.

Desirable

  • Expertise in one or more specific genomic technology.
  • An understanding of programming, particularly regarding big data, data visualisation and data-mining techniques within a genomic setting.
  • Knowledge of research areas relevant to Crick research.
  • Basic knowledge of molecular biology.
  • Experience in bioinformatics training.

Crick lab/facility