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GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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GraphMap ONT parameters #92

Open npavlovikj opened 6 years ago

npavlovikj commented 6 years ago

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

msikic commented 6 years ago

Hi Natasha,

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

Best

Mile

npavlovikj commented 6 years ago

Thank you!