Genomics Bioinformatician
Genomics Bioinformatician
Basecamp Research
Farringdon, United Kingdom
The Role
The successful candidate will take ownership, expand and manage our sequencing and metagenomic data analysis production operations in the first instance.
- They will have the opportunity to investigate new methods to maximize the curation and annotation of the microbial dark matter, and our unique sequencing datasets
- This will be a strong collaborative role working closely with all teams at all data collection and analysis points. This will include but not limited to our biodiversity partners, field scientists, sequencing ops, ML scientists, data engineers and commercial stakeholders.
Responsibilities
Develop and run software to support the genome collection and sequencing operations, post curation and labelling of data and the overall goals of the Genomics team. Our sequencing data stack includes second and third generation technologies.
Responsibilities may include, in coordination with other team members:
- Taking ownership in building, improving and managing the in-house genomic assembly and annotation pipeline. This will entail:
- Manage and audit the data workflow of our samples from collection to data warehousing. This includes the quality control of appropriate files and datasets
- Collaborate with the Data Engineering team in building and managing the pipeline in our in-house designed infrastructure platform
- Investigate, benchmark and integrate novel analyses into the pipeline
- Write and document high quality code and methodology of processes
- Methods development to leverage the in-house sequencing datasets to create full high quality genomes for context analysis
- Contribute to problem-solving discussions within and across teams to generate ideas that will benefit all aspects of the organisation
- Opportunity to lead from the front when it comes to bringing new ideas and approaches to the table
Required skills and experiences
- A graduate (MSc/PhD) degree in the life sciences, computer science or similar
- At least three years of post bachelors experience in the life science and genomics, preferably in industry or a high throughput research institute
- Have directly worked in an environment that involved processing hundreds to thousands of samples. This is beyond just downloading from the public databases but handling data at the raw level and the ability to track each datapoint:
- if microbial or metagenomics have demonstrated managing in the upper hundreds
- if human or clinical resequencing have demonstrated managing in the thousands
- Have experience writing complex pipelines using workflow languages and tools for genomic and protein analysis and have demonstrated the ability to benchmark what to choose for each step of a pipeline:
- Dagster > Nextflow > Snakemake > Stepfunctions > other
- Have worked with environmental metagenomic or microbiome datasets. This means not one single organism, or parasite or cultured bacterium
- Have extensive experience working with second and third generation sequencing datasets for downstream analysis:
- Experience with methods development with sequencing read datasets
- Proficient at using unix based operating systems, libraries, and tools
- Knowledge and experience of tools used in bioinformatics both in genomics, metagenomics and/or protein biology
- Proficiency with a programmatic scripting language (python, bash etc.)
- Excellent analytical and problem solving skills
- Excellent communication skills and ability to work closely with interdisciplinary teams
- Fluency in English
Advantageous skills and experiences
- Have worked and developed analysis/methods with population sequencing data or analysing variation within metagenomic sequencing data
- Have worked with novel deep learning methodology in analysing genomic data
- Have worked in developing novel computational methods or analyses towards the annotation of phage, viral and/or archaea genomes
- Experience in the techbio/biotech industry that is focused on product development (therapeutics, protein/drug discovery, CRO etc.)
- Experience with building databases (relational and/or non-relational)
- Experience using a HPC environment
- Experience using cloud solutions (AWS, GCP etc.)
- Experience with containerization (Docker, Singularity)
- Experience with git and Gitlab or Github
- Experience with Agile software development
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