Canu

Category

Bioinformatics, Assembly pipeline

Description

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION). Canu is a hierarchical assembly pipeline which runs in four steps:

Detect overlaps in high-noise sequences using MHAP

Generate corrected sequence consensus

Trim corrected sequences

Assemble trimmed corrected sequences

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
		1.2

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
1.2	module load new gcc/4.8.2 python/2.7.6 java/1.8.0_31 canu/1.2	openblas/0.2.13_seq

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a canu job in batch mode with the following command:

bsub [LSF options] "canu [canu options]"

Here you need to replace [canu options] with canu command line options and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system.

License information

GPLv2

Links

http://canu.readthedocs.io/en/latest

https://github.com/marbl/canu