Welcome to the wiki of the SIB training: Bioinformatics of Long Reads Sequencing 2017 !

Long Reads Workshop

This material should provide a first-steps support on how to operate with long reads using command line tools. The goal is to provide a starting point for researchers that are familiar with next generation data and Unix operations but new to long read sequencing.

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Table of content

• Contributors
• Practical Information
  • Run docker image
  • Unix: useful tips
• Introduction
  • Learning objectives
  • Pacific Biosciences: RSII
  • Oxford Nanopore Technologies: MinION
  • Biological material
  • File organization
  • Checkpoint
• Experimental design
• Read extraction
  • TUTORIAL: Extraction of MinION reads
  • TUTORIAL: Extraction of PacBio reads
  • Checkpoint
• Genome assembly
  • Choice of assembler
  • TUTORIAL: assembly using Canu
  • TUTORIAL: assembly using Miniasm
  • Polishing
  • Checkpoint
• Transcriptome assembly
  • TUTORIAL: PacBio Iso-Seq pipeline
  • TUTORIAL: error correcting MinION 2D reads with Canu
  • Checkpoint
• Assessing quality of genome assembly
  • TUTORIAL: Reference-based metrics
  • Continuity metrics
  • Completeness metrics
  • Contamination
  • Checkpoint
• Assessing quality of transcriptome assembly
  • TUTORIAL: Align the experimental transcripts to the reference genome
  • TUTORIAL: Compare the experimental transcripts to the reference annotation
  • Checkpoint
• Post-assembly steps
  • TUTORIAL: Anchoring contigs and scaffolds using linkage maps
  • Checkpoint
• Acknowledgements

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