Difference between revisions of "Canu"
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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
