Assembly with WGS dataset(2)¶
Generate corrected reads¶
The command to run the canu correction is:
canu
with the following parameters:
| What? | parameter | Our value |
|---|---|---|
| The input read file | -nanopore-raw | ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz |
| The output directory | -d | ~/workdir/assembly/assembly_wgs/ |
| 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 |
The complete command is:
canu -d ~/workdir/assembly/assembly_wgs/ -p assembly useGrid=false -nanopore-raw ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz genomeSize=30k minReadLength=300 minOverlapLength=20