Polishing with medaka(2)¶
We call:
medaka_consensus
with the following parameters:
| What? | parameter | Our value |
|---|---|---|
| The input read file | -i | ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz |
| The racon polished assembly | -d | ~/workdir/assembly/assembly_wgs/racon.fasta |
| The output directory | -o | ~/workdir/assembly/assembly_wgs/medaka |
| Number of threads | -t | 14 |
| The model | -m | r941_min_high_g360 |
The complete commandline is:
medaka_consensus -t 14 -m r941_min_high_g360 -i ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz -d ~/workdir/assembly/assembly_wgs/racon.fasta -o ~/workdir/assembly/assembly_wgs/medaka
In a next step, we will use quast to compare our assemblies.
If medaka_consensus fails with an error massage try the following an re-run the command above:
pip install tensorflow