Hands-on Workshop on Nanopore Sequencing:
Adventures in Metagenomics and Antimicrobial Resistance

Date: 25—29 Nov 2019
Location: Indian Institute of Technology, Delhi, India
Sample collection: Week before the workshop in Uttarkashi

Antibiotics increasingly fail to treat a growing number of medical conditions due to antimicrobial resistance. This trend is especially acute in developing countries such as India, where broad resistances are known to have emerged. It is known that densely populated cities can drive the emergence and spread of antimicrobial resistance through for example industrial production sites, wastewater management practices and other cultural characteristics. Proximity to waterways or associated water collections seems especially relevant.

This workshop is part of the BMBF – DBT Cooperative Science Program: Development of metagenomics assisted surveillance tools for tracking antibiotic resistance in river bodies — A study in the Ganges river valley (NANOLOG). The focus of the study is to investigate samples from river Ganges in India to infer the effect of human interference and to discern naturally occurring resistance from resistance created by humans.

The workshop will provide a platform for technology transfer and direct interaction with researchers in India. During the workshop, water and sediment samples collected before (pristine site) and after Uttarkashi will be analyzed using Nanopore sequencing to assess the effect of human settlement on the quality of water in terms of bacterial load.


For registration, please send an email to including the following information:
Name, affiliation, email address, short CV, and wet-lab and/or bioinformatics experience.
Please use the subject “[Registration] Hands-on Workshop on Nanopore Sequencing”.

Registration deadline: 15 November 2019
Registration is limited to 15 participants.

Speakers and Organizers

Preliminary Workshop Programme

Monday, 25 November

10:00 amWelcome note by Prof. Shaikh Z. Ahammad
10:20 amChristoph Lübbert
11:00 amChristian Brandt
11:40 amMartin Hölzer
12:20 pmSebastian Krautwurst
01:00 pmLunch
02:30 pmFlowCells and MinIONs
 Group 1Group 2Group 3
Christian BrandtCelia DiezelAkash Srivastava
Tuesday, 26 NovemberStart with DNA isolation (Culture)Start with Library prep (on-site DNA)DNA isolation (amplicon)
Wednesday, 27 NovemberStart with Library prepDNA isolationStart with Library prep

Thursday, 28 November

Setting up the Laptop.
Introduction to Docker, bash, etc.
Basecalling the data

Friday, 29 November

Assembly, analysis and troubleshooting tips
General discussion, Q/A, and closing remarks