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Live mapping Nanopore fastq with minimap2?

Hi Biostars community,

I am new to the world of bioinformatics and looking for a simple method to live map MinKnow GPU called fastq files using minimap2. Essentially, I am after a way of having minimap2 'monitor' a folder, and as completed fastq files appear, they are mapped to the reference fasta files in real-time with minimap2.

I hope you can point me in the right direction. Thanks in advance!

Cheers, Gusto

guppy minimap2 live nanopore
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updated by GenoMax GenoMax • written by Gus • Gus

Isn't read_until_api from Nanopore (LINK) enabling this?

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written by GenoMax GenoMax

1 answer

Interesting idea.

entr https://github.com/eradman/entr is the first dedicated standalone tool I have seen for triggering a command if files change.

Essentially it's a devops problem, start a build process if source files change on disk (jenkins etc).

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written by colindaven colindaven

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