Edgardo Ortiz and Hanno Schaefer from the TUM in Freising will offer a hands-on “Nanopore for the field” workshop on 8th to 10th February 2023 with a maximum of 15 participants.

 

If you are interested in this method, you can register here until December 23, 2022:

https://forms.gle/sF9yE3L45kjC68dk8

 

Detailed Information

Nanopore sequencing is a cheap and fast way to produce sequence data in and outside the lab. With a relatively simple bioinformatics set-up, everybody can produce barcoding sequences and even full organellar genomes and nuclear genome fragments of reasonable quality. In our workshop, we introduce our simple protocol for sequencing multiplexed barcode regions under field conditions and how to analyze such data. The second topic will be the sequencing of organellar genomes or large nuclear genome fragments using Nanopore. We will discuss the advantages and disadvantages of Nanopore for different approaches and the challenges we have faced.

 

We work mainly with vascular plants, but we welcome participants who are interested in different organismal groups. Participants who want to sequence their own DNA samples should get in touch with us early to discuss specific needs (e.g., barcoding primers). In this workshop, we will not discuss metabarcoding strategies (e.g., for bacterial films or soil crusts) and direct RNA-sequencing of Viruses.

Participants are expected to have some experience with lab work and analysis of sequence data, but prior Nanopore or programming experience is not required.

 

Preliminary Program

Wednesday, 08.02.2023, 10:00-18:00

Short talks

  • Introduction to Nanopore (theory of sequencing and assembly)

  • Challenges for field-based approaches

  • Overview of the barcoding protocol

Hands-on

  • Library prep for multiplexed barcoding run

  • Loading of flow cell

  • Start Nanopore runs (with simultaneous basecalling)

 

Thursday, 09.02.2023, 09:00-18:00

Short talk

  • Overview of the analysis pipeline (NanoAmp)

Hands-on

  • Analysis of run data (demultiplexing, quality control)

  • Library prep for plastome/genome sequencing

  • Loading of flow cell

  • Start Nanopore runs (with simultaneous basecalling)

Friday, 10.02.2023, 09:00-16:00

Short talk

  • Advantages and disadvantages of genome sequencing with Nanopore

Hands-on

  • Plastome/genome assembly


For further information regarding the workshop contact

Edgardo Ortiz (edgardo.ortiz@tum.de)

Hanno Schaefer (hanno.schaefer@tum.de)