Learning - aechchiki/SIB_LongReadsWorkshop_Zurich18 GitHub Wiki

Learning Objectives

Section: Practical Information [3/4].

Aim

The aim of this practical session is to get your hands on real data (DNA/RNA) generated from two long-reads sequencing platforms:

  • Oxford Nanopore (ONT) MinION
  • Pacific Biosciences (PacBio) RSII

At the end of this practical, you should be able to:

  • get an overview of the sequencing platforms, the sequencing method behind data generation
  • biological applications and the main advantages/pitfalls of using long-reads as compared to short-reads
  • extract reads in standard format from native technology-specific format
  • align the extracted reads to the reference genome/transcriptome
  • use the extracted reads to assemble the genome and the transcriptome
  • compare your assemblies to the reference for the analyzed species
  • get an overview of downstream analysis you could apply on your assemblies
  • understand the usage and theory behind the software you will be using here
  • decide which combination of platform/method is best for a given biological goal

Need ECTS?

If so, please let us know as soon as possible, so that we can planify the exam procedure in function of the number of candidates.

(An idea could be to schedule the exam on Nov 9th, after lunch & before Weihong's session?)

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