Difference between revisions of "Canu"
| Line 11: | Line 11: | ||
curl -L -o oxford.fasta http://nanopore.s3.climb.ac.uk/MAP006-PCR-1_2D_pass.fasta | 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'''. | + | As you can see, this is a 2D data set. The downloaded file will be calle '''oxford.fasta'''. |
| − | canu -p ecoli -d ecoli- | + | The recommended way to run '''canu''' for this is: |
| + | |||
| + | canu -p ecoli -d ecoli-oxfordgenomeSize=4.8m -nanopore-raw oxford.fasta | ||
| + | |||
| + | <ins>Explanation</ins>: | ||
| + | * '''-p''', a prefix | ||
Revision as of 18:25, 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.
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
