Scientist, Community Sequencing, USA

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 primary objective of the Scientist will be to work on community sequencing analysis from crop plants and soil. This will include characterize plant and soil associated microbial populations to understand their functions, interactions and ecology. The Scientist will work closely with other functional teams in Discovery (Microbial Evaluation and RTP) as well as Data Sciences, IP and IT teams.


  • Functional profiling of complex microbial communities from crop plants and soil
  • Run community sequencing pipeline and deep dive analyses to identify over represented strains in specific crops, treatments, and stresses
  • Generate data-driven hypotheses for strain isolation
  • Work closely with Data Sciences Team to ensure proper taxonomic identification, review current analysis pipeline and suggest improvements
  • Propose biological and computational protocols to analyze the community structure of the plant microbiome
  • Work closely with IT and Data Management to ensure data and metadata are properly captured and stored in database


  • Knowledge of existing bioinformatics tools and databases and a creative mindset to adapt them to biological questions and analyses
  • Strong desire to continue learning, identify new techniques and technologies, and rapidly implement them to keep Indigo at the cutting edge
  • Agile with the ability to deliver in a fast-paced environment and shift priorities quickly
  • Excellent oral and written communication in both Biology and Computational terms including strong presentation skills
  • Passion for Indigo and our core values
  • Self-starter to propose new ideas
  • Team player, works well across teams, collaborative
  • Proactive, well organized and independent while also being supportive of other groups


  • PhD and 1-2 years’ experience (plant or soil related field, computational biology or equivalent)
  • Hands on experience with community sequencing or metagenomics experiments
  • Experience in design of quantitative biological experiments to test scientific hypotheses in greenhouse/field
  • Experience in performing computational analyses of large data sets and biological interpretation of quantitative analyses
  • Experience in designing and scripting pipelines to analyze sequencing data
  • Strong statistical background
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