Live mapping Nanopore fastq with minimap2?
1
0
Entering edit mode
5 weeks ago
Gus • 0

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 • 215 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
5 weeks ago
colindaven ★ 3.3k

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).

ADD COMMENT

Login before adding your answer.

Traffic: 2455 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6