Portable, single-molecule sequencing is the technology of today and tomorrow. Its countless applications, especially in precision medicine, stimulate the imagination - sequencing can now reach beyond the sophisticated labs. We plan to undertake four parallel projects at #NGSchool2018:

  1. sequencing and de novo assembling the genomes of previously unsequenced organisms
  2. metagenomics of oral microbiomes including volunteers from the course, so you can sequence and analyse your own oral microbiome
  3. direct RNA-seq & de novo transcriptome assembly of non-model fish species
  4. and human genomics (depending on external funding)

Participants will be divided into small groups (~10 people) and each project will be assigned a mentor, an expert from the field. Students will conduct the whole experiment, starting from sample preparation, through sequencing and data analysis to report writing. We plan to meet daily for updates of every project progress, data analysis and troubleshooting. Importantly, sequenced genomes will be deposed in the public database and the reports and results will be published.

Outline

We will do sample prep in the afternoon, sequencing overnight and data analysis the next morning (in total 26 hours reserved). Our initial schedule divided by days:

  1. Theoretical introduction to Nanopore sequencing [3h] & Sample preparation and sequencing run overnight [3h]
  2. First batch of sequencing data ready, basecalling, QC, preliminary analysis [3h]
  3. Second batch of sequencing data ready, basecalling, QC, de novo genome assembly [3h]
  4. De novo genome assembly [4h]
  5. Gene prediction and functional annotation [4h]
  6. Report writing and data deposition to public databases [3h]
  7. Summary, team presentations [3h]

Mentors

Experimental experts:

  • Jan Gawor, IBB, Warsaw, PL

  • Monika Gos,  IMC, Warsaw, PL

  • Viktória Hodorová & Hana Lichancová, Comenius University, SK

  • Monika Mańkowska-Woźniak, GenXone, PL

  • Eugeniusz Tralle, IIMCB, Warsaw, PL

  • Natalia Zawrotna, CeNT UW, Warsaw, PL

Data analysis experts: