Canu

Introduction

This is the de-novo genome assembler for long read technologies: mainly PacBio and Oxford Nanopore (MinION).

It comes from the Maryland Bioinformatics Laboratory, and is based on the Celera Assembler.

Example Usage

The following use Nick Loman's Ecoli data file which can be obtained via:

curl -L -o oxford.fasta http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta

As you can see, this is a 2D data set. The downloaded file will be calle oxford.fasta.

The recommended way to run canu for this is:

canu -p ecoli -d ecoli-oxfordgenomeSize=4.8m -nanopore-raw oxford.fasta

Explanation:

• -p, a prefix