GraphMap ONT parameters

[Natasha Pavlovikj]

Hi,

I am comparing few nanopore aligners on ONT 1D and ONT 2D data, so I would like to verify if the general command below is correct for those types of reads
graphmap align -r ref.fasta -d input.fasta -o output.sam
or I need to specify some other parameters as well.

I would highly appreciate your input on this.

Thank you,
Natasha

[Mile Sikic]

Hi Natasha,

You are right. This is the correct command. Other parameters depend on specific use cases such as circular genomes, etc.

Best

Mile

[Natasha Pavlovikj]

Thank you!