What ML, NN based variant callers work on Galaxy servers?

1

Need an AI ML based variant calling tools for Illumina and Oxford data, please. Is there any Galaxy instance I could not find?

2

Hi,
You can find all available tools and their description in the Gaxy Tool Shed.

3

Hi @player_777,
I think that there’s not currently any tool with those characteristics. Have you in mind any of them? We can create the tool wrapper if required.

Regards

4

DeepVariant,

thanks

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5

DeepSV
DAVI
Clarivoyant
Variant Works
CoVacs are also good tools to see on Galaxy

6

Thanks! I’ll start working in DeepVariant and will include the rest in the tool request list. I will try to make it available for next week.

Regards

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7

Where I can access these tools now? Thanks

8

Hi!
I’m still working on it. I’ll try to make it available for the next week.

Regards

9

Is there any progress and results available? Thanks.

10

HI @player_777,
I’ll try to make it available this week.

Regards

11

Hi @player_777,
I have opened a PR for including the DeepVariant tool DeepVariant PR.

Regards

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12

Thank you. Please put your tools to the https://usegalaxy.eu/ and https://nanopore.usegalaxy.eu/.

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13

Please put your tools to the https://usegalaxy.eu/ and https://nanopore.usegalaxy.eu/ .

Thank you.

14

Hi @player_777,
I didn’t include it in the nanopore.usegalaxy.eu instance because this specific tool wrapper doesn’t support nanopore reads; it requires to include an specific DeepVariant version. If you need to work specifically with nanopore reads, let me know and I’ll include the required modifications.

Regards

15

What Galaxy instance has DeepVariant now? I have Illumina and IonTorrent data too. Thanks.

16

I have found it as DeepVariant deep learning-based variant caller (Galaxy Version 1.2.0+galaxy1) there now. Please make settings for Oxford nanopore long reads and hybrid Illumina plus ONT and Ion Torrent there. We have SARS-Cov-2 and Tuberculosis genomes for processing. Producing some charts/figures would be an advantage. Thank you.