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Genome Assembly: Canu

Canu paper

What is N50?

Tutorial adapted from Canu Quick Start Guide: https://canu.readthedocs.io/en/latest/quick-start.html

DO NOT run

  1. Get tutorial nanopore data for E. coli
curl -L -o oxford.fasta http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta
  1. Run Canu
canu -p ecoli -d ecoli-oxford  genomeSize=4.8m maxThreads=8  -nanopore-raw oxford.fasta

Examining results

Most of what you will be interested in the contigs files in the ecoli-oxford folder.

Try:

 grep ">" ecoli-oxford/ecoli.contigs.fasta

How many contigs did we find and how big are they?

Explore Canu for your samples

Between now and Monday attempt a Canu run on your data.

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