Bioinformatics Consultant

Indigo is a company dedicated to harnessing nature to help farmers sustainably feed the planet. With a vision of creating a world where farming is an economically desirable and accessible profession, Indigo works alongside its growers to apply natural approaches, conserve resources for future generations, and grow healthy food for all. Utilizing beneficial plant microbes to improve crop health and productivity, Indigo’s portfolio is focused on cotton, wheat, barley, corn, soybeans, and rice. The company, founded by Flagship Pioneering, is headquartered in Boston, MA, with additional offices in Memphis, TN, Research Triangle Park, NC, Sydney, Australia, Buenos Aires, Argentina, and São Paulo, Brazil.

The Bioinformatics Consultant will work with the R + D Data Science team to drive innovation throughout R + D by turning sequencing data into scientific insights.  They will support an ongoing academic collaboration to help comprehend the vast diversity of fungi by running Indigo’s annotation pipeline on whole-genome sequencing data and facilitate bioinformatics analyses of the annotation data, including comparative genomics.  The ideal candidate will apply biological expertise to sequencing and annotation data to generate insights for scientists.  The role also requires communication with laboratory scientists and end users of sequencing data to solve their problems with cutting edge bioinformatics and computational biology tools.  We desire a curious and driven scientist who is always looking to implement the best recent technical advances to advance Indigo’s R + D pipeline.



  • Assemble and annotate genomes using Indigo’s custom pipelines:
    • Ensure quality of assemblies and annotation coverage and report relevant metrics
    • Catch errors and troubleshoot problems – determine which originate in sequencing data and which are computational
    • Examine results to find any patterns of mis-assembly or annotation that should be corrected
  • Provide ad-hoc bioinformatic analyses to support Indigo’s academic collaborators including:
    • Comparative genomics of strains using annotation results
    • Comparison with public datasets
    • Reshaping data to fit collaborator needs
    • Help our scientists understand genomic signatures of pathogens vs endophytes
  • Work with Indigo scientists to implement metabolic analyses:
    • Test new analyses developed by Indigo’s bioinformatics team on relevant strains
    • Assist with the curation of relevant metabolic pathways
    • Suggest other annotation resources or analyses as necessary


Competencies and Qualifications:

  • Experience in:
    • Running bioinformatics pipelines
    • Existing bioinformatics/DNA Analysis tools and work flows
    • Pathway identification and comparative genomics
    • Working with annotation databases and other resources
    • Comfortable querying and working with databases
    • Coding in Python and/or R
    • Comfort with UNIX and AWS 
  • Knowledge of existing bioinformatics tools and databases and a creative mind to adapt them to new problems and analyses
  • Deep knowledge of cell biology especially metabolism
  • Focused on customer satisfaction, especially laboratory scientists, and experience working directly with stakeholders to implement exactly what the customer needs
  • Team player, great teaching skills, and excellent communication skills
  • A creative mind and interest in Indigo’s work and mission.
  • PhD or doctorate in progress, or Masters in Bioinformatics, Comp Bio or relevant field with at least 2-5 years of experience working with sequencing datasets
  • Experience writing code to solve biological problems in Python (preferred) or R or other programming language (e.g. MATLAB, Java, etc.)


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