tools for nanopore data analysis

usegalaxy.eu support
1

I wonder what tools in galaxy europe can be used for nanopore data analysis? Thanks.

Best regards,
Chen

2

If you search for “nanopore” in the tool menu you will get some results. I think there are more tools that can be used on this type of data (like more general text edit tools etc.). Does this help?

Maybe you can tell what you are specifically looking for and someone can give a more detailed answer.

This can also help:

1 Like
3

I have fastq files for HIV drug resistance test (gene mutation identificatin) from nanopore platform. I wonder how to analyze the fastq files by galaxy europe? Thanks.

Best regards,
Chen

4

I try to assemble fastq reads using Flye tool, but failed, see below:

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. I wonder why it is like this? Thanks.

Best regards,
Chen

5

Hi @huiping

First, try a rerun to eliminate some transient cluster error.

Next, assembly is in particular sensitive to read content. The error logs for the tool might have captured some of those details, but checking the read quality directly is more actionable. Meaning, the plots generated might have clues.
Ref: https://training.galaxyproject.org/training-material/search2?query=resistance

Please give those a try, then if you get new errors, you can link back the Job Details page (expand the dataset and copy the link from the “i” information icon) or better, share the entire history so others can review the QA too.