Polishing with Racon(2)¶
We call racon:
racon
with the following parameters:
~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz
~/workdir/mappings/Cov2_HK_WGS_small_porechopped_vs_wuhan.sam
~/workdir/wuhan.fasta
| What? | parameter | Our value |
|---|---|---|
| The input read file | positional (1) | ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz |
| The mapping file | positional (2) | ~/workdir/mappings/Cov2_HK_WGS_small_porechopped_vs_assembly_wgs.sam |
| The reference file | positional (3) | ~/workdir/assemmbly/assembly_wgs/assemby.contigs.fasta |
| Number of threads | -t | 14 |
| Racon parameters for medaka | -m 8 -x -6 -g -8 -w 500 | |
| Output file | forward with “>” | ~/workdir/assembly/assembly_wgs/racon.fasta |
Then we can call racon with our mapping, the read file and the assembly file. We use 14 threads to do this:
racon -m 8 -x -6 -g -8 -w 500 -t 14 ~/workdir/data_wgs/Cov2_HK_WGS_small_porechopped.fastq.gz ~/workdir/mappings/Cov2_HK_WGS_small_porechopped_vs_assembly_wgs.sam ~/workdir/assembly/assembly_wgs/assembly.contigs.fasta > ~/workdir/assembly/assembly_wgs/racon.fasta