Canu
From ScientificComputing
Contents
Category
Bioinformatics, Assembly pipelineDescription
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 sequencesAvailable versions (Euler, old software stack)
Legacy versions | Supported versions | New versions |
---|---|---|
1.2 |
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 |
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.