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treangenlab / lemur

Lemur is a tool for rapid and accurate taxonomic profiling on long-read metagenomic datasets
MIT License
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Lemur + Magnet #13

Open humbleflowers opened 2 months ago

humbleflowers commented 2 months ago

Hello developers,

Thank you for the tool.

I am working on shotgun ONT metagenomics data and came across your tool and bioarxiv paper.

I ran lemur but i am struggling to find information on magnet and command line used in the paper.

Can you pls give me some instructions on magnet?

Thank you.

nsapoval commented 2 months ago

Thank you for reaching out. We have recently update the Magnet repository and included relevant instructions. For the general reference, the command used to run magnet with Lemur output as in the manuscript is:

magnet.py -c {lemur_report_file} -i {input_fastq_file} -o {output_path} -m ont

You can find additional details in the Magnet repo.

Please let us know if this resolves the issue or if you encounter any further roadblocks.