Assembly with canu(3)

Run trimming and assembly

The command to run the canu trimming and assembly is:

canu -trim-assemble

with the following parameters:

What? parameter Our value
The input read file -nanopore-corrected ~/workdir/assembly/small_correct/assembly.correctedReads.fasta.gz
The output directory -d ~/workdir/assembly/small_assembly
Prefix for output files -p assembly
Use a grid engine useGrid false
Genome Size genomeSize 30k
Minimum Read Length minReadLength 300
Minimum Overlap Length minOverlapLength 20 or try out different value
Optional: Coverage of corrected reads corOutCoverage something smaller than our coverage (~600)
Optional: Min coverage for corrected reads corMinCoverage 0 to get all
Optional: Correction Sensitivity corMhapSensitivity normal

The corOutCoverage parameter defines to which coverage the reads are corrected, longest reads are corrected first. It is advisable to set this parameter high, to get more sequences into the assembly. corMinCoverage set to low value, will report low covered reads as well and corMhapSensitivity=normal is advised for higher coverage.

The complete command is:

canu -trim-assemble -d ~/workdir/assembly/small_assembly -p assembly useGrid=false -nanopore-corrected ~/workdir/assembly/small_correct/assembly.correctedReads.fasta.gz genomeSize=30k minReadLength=300 minOverlapLength=20

In the next step, we will evaluate our assembly.