Difference between revisions of "Canu"

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(Created page with "= Introduction = This is the de-novo genome assembler for long read technologies: mainly PacBio and Oxford Nanopore (MinION). It comes from the Maryland Bioinformatics Labor...")
 
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It comes from the Maryland Bioinformatics Laboratory, and is based on the Celera Assembler.
 
It comes from the Maryland Bioinformatics Laboratory, and is based on the Celera Assembler.
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= Example Usage =
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The following use Nick Loman's Ecoli data file which can be obtained via:
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curl -L -o oxford.fasta http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta
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As you can see, this is a 2D data set. The downloaded file will be calle ''oxford.fasta'''.
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canu -p ecoli -d ecoli-oxford genomeSize=4.8m -nanopore-raw oxford.fasta

Revision as of 17:17, 9 March 2017

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'.

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