Andrew Severin

Andrew Severin

His PhD was in Biophysics/NMR spectroscopy. He did a Bioinformatics Postdoc in Soybean genetics and now runs the Genome Informatics Facility at Iowa State University. He is passionate about evolution and the science behind the genome. There is so much we don't know about how the elements in a genome interact to create the fine balance of gene expression, modification and 3D structure that create the dynamic range of phenotypes we observe. As sequencing technology continues to improve and the cost continues to decrease, we will be able to ask more complex questions that increase our understanding via comparative and translational genomics.

Background

Canu Steps

  • The Canu Assembler has three steps
    • Correct (-correct)
    • Trim (-trim)
    • Assemble (-assemble)

    These steps can be run individual if you specifiy the (-step) parameter as defined in parenthesis above or these steps will be all run if no step parameter is specified.

How to run Canu

  • Canu parameter considerations

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    Trio binning
  * If you have sequence data from the parents and the F1 offspring
Raw Data type requires a different parameter to read each datatype
  * PacBio
  * Nanopore
Coverage
  * Low Coverage parameters can be set to improve assembly output depending on the sequencing technology See [Canu Quick Start Guide](http://canu.readthedocs.io/en/latest/quick-start.html) for more details.
Canu Basics
  * -p is the assembly prefix and this is the name that will be prefixed to all output Files
  * -d is the directory that it will make and write all the files to.
input file types (multiple files can be listed after this parameter but should be of the same type)
    * -pacbio-raw
    * -pacbio-corrected
    * -nanopore-raw
    * -nanopore-corrected

  • Running Canu

    The name of the module will vary here and you should check to see what version you are using.

  • Example SLURM Job

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    #!/bin/bash
#SBATCH --nodes=1
#SBATCH --time=24:00:00
#SBATCH --mem=64G
#SBATCH --mail-user=YOUREMAILADDRESS
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
#SBATCH --error=JobName.%J.err
#SBATCH --output=JobName.%J.out
module load canu

canu -p Bt2 -d Bt2_assembly genomeSize=6.2m  -pacbio-raw SRR2093876_subreads.fastq.gz

Expected files generated during assembly

Files output from assembly
Bt2.contigs.fasta Bt2.contigs.gfa Bt2.contigs.layout
Bt2.contigs.layout.readToTig Bt2.contigs.layout.tigInfo Bt2.correctedReads.fasta.gz
Bt2.gkpStore Bt2.gkpStore.err Bt2.gkpStore.gkp
Bt2.report Bt2.trimmedReads.fasta.gz Bt2.unassembled.fasta
Bt2.unitigs.bed Bt2.unitigs.fasta Bt2.unitigs.gfa
Bt2.unitigs.layout Bt2.unitigs.layout.readToTig Bt2.unitigs.layout.tigInfo
canu.out canu-logs canu-scripts
correction trimming unitigging

SLURM standard output

  • An example of the output log can be found here: canu.out

Errors

Further Reading

Back to the Assembly and Annotation Index page