Hi Vineet!

What analysis are you looking at ?

There are several tools designed for specific applications.

Basecalling: Guppy (Guppy GPU is much faster but you'll require a decent Nvidia GPU)

Demultiplexing: QCAT

Quality Control: pycoQC, NanoFilt

Alignment: NGMLR, minimap2

Variant calling: NaoPolish, Medaka, Clair

Structural variant calling: Sniffles

All these tools are Linix/Unix only.

Plus there are several tools for specific applications. It'll all depend on your use case.

Hope it helps!

Thank You Aditya,

Basically I'm looking for QC, ALIGNMENT and demultiplexing.

So I've mentioned the tools above for the specific purpose. Go ahead and give them a spin.

May the science be with you!

Hi Aditya....

any recommendation for software for windows ?

Hi Amro!

On Windows, you may use GUPPY basecaller that comes along with the MinKNOW software package. It'll give you base called FASTQ files if you select base calling along with sequencing in real time. Keep in mind that you'll require a decently powered workstation and SSD with around 1 TB of free space (depending on your experiment) for this purpose. By decently powered I mean at least a system with 4 cores-8 threads, 16 GB of RAM and possibly a compatible NVIDIA GPU.

I would still recommend you to install Linux or Windows Subsystem for Linux (WSL) if you're running Windows 10 and do not wish to install Linux as a whole.

Read about WSL, and you'll have almost all tools running on your Windows itself.

Hope it helps.

May the science be with you!

Thank you Aditya Singh I am new to this but I will do my research work. Much appreciated.

Hi Aditya Singh, we have ran some Coronavirus samples on MinION using MinKnow with the Guppy basecaller on; then we had to re-run to get enough reads, however, on this second time we left the Guppy off. All these using windows 10. At this point, we´re left with two sets os reads (one not basecalled, yet).

How do I run this last data on Guppy separately, using windows instead of using command line?

Thank you for the help

Regards

Hi Flavio!

Maybe I'm late in responding and you've already done it by now, but here it is:

You can use MinKNOW to perform this analysis.

Use the analysis module of MinKNOW and select basecalling, point it to the folder and run. You'll have your basecalled FASTQ files.

I hope this helps.

Hi Aditya,

Your response is still In good time.

Thanks a lot for the help. I'll try it out.

Kind regards

you can use https://usegalaxy.org/.