Canu-Teaching
Category
Bioinformatics
Program On
Teaching
Version
1.4
Author / Distributor
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" More details are at canu
Running Program
The last version of this application is at /usr/local/apps/eb/canu/1.4-foss-2016b
To use this version, please load the module with
ml canu/1.4-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_canu
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=canu.%j.out
#SBATCH --error=canu.%j.err
cd $SLURM_SUBMIT_DIR
ml canu/1.4-foss-2016b
canu [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml canu/1.4-foss-2016b canu -h usage: canu [-correct | -trim | -assemble | -trim-assemble] \ [-s <assembly-specifications-file>] \ -p <assembly-prefix> \ -d <assembly-directory> \ genomeSize=<number>[g|m|k] \ errorRate=0.X \ [other-options] \ [-pacbio-raw | -pacbio-corrected | -nanopore-raw | -nanopore-corrected] *fastq By default, all three stages (correct, trim, assemble) are computed. To compute only a single stage, use: -correct - generate corrected reads -trim - generate trimmed reads -assemble - generate an assembly -trim-assemble - generate trimmed reads and then assemble them The assembly is computed in the (created) -d <assembly-directory>, with most files named using the -p <assembly-prefix>. The genome size is your best guess of the genome size of what is being assembled. It is used mostly to compute coverage in reads. Fractional values are allowed: '4.7m' is the same as '4700k' and '4700000' The errorRate is not used correctly (we're working on it). Don't set it If you want to change the defaults, use the various utg*ErrorRate options. A full list of options can be printed with '-options'. All options can be supplied in an optional sepc file. Reads can be either FASTA or FASTQ format, uncompressed, or compressed with gz, bz2 or xz. Reads are specified by the technology they were generated with: -pacbio-raw <files> -pacbio-corrected <files> -nanopore-raw <files> -nanopore-corrected <files> Complete documentation at http://canu.readthedocs.org/en/latest/ ERROR: Invalid command line option '-h'. Did you forget quotes around options with spaces? ERROR: Assembly name prefix not supplied with -p. ERROR: Directory not supplied with -d. ERROR: Invalid 'corErrorRate' specified; must be set ERROR: Required parameter 'genomeSize' is not set
Installation
Source code is obtained from canu
System
64-bit Linux