Shotgun metegenomics analysis on google colab

[Ktalaat55 (Kareem Ismail)]

Hello,
I'm having trouble finding a guide on how to analyze shotgun metagenomics data using QIIME 2 on google coab. Specifically, I'm looking for a tutorial that takes raw sequencing data and converts it into a matrix showing sample IDs and abundances and explore diversities. If anyone knows of such a resource, I'd be very grateful
Thanks all

[Nicholas_Bokulich]

Hi @Ktalaat55 ,

DId you check the tutorials page of the forum? Please see here:

draft tutorial for shotgun metagenomics with QIIME 2

Hi all, Following on our announcement of the first alpha release of the QIIME 2 Shotgun Metagenomics Distribution, we are starting to develop some alpha (early draft) tutorials. At the moment, we're going to keep these on GitHub and link to specific documents that you can view there. Before too long, we'll be starting to build and host Jupyter Books that cover tutorials for the different QIIME 2 distributions that are available. So, here's a first iteration of a bring-your-own-data tutorial co…

Diversity analyses are not included, but once you have a feature table you can do diversity and other analyses as described in the regular QIIME 2 tutorials on qiime2.org

Good luck!

[Ktalaat55 (Kareem Ismail)]

Thanks for your reply. Yes, I have followed tutorial but I got the following " Error: QIIME 2 has no plugin/command named 'classify-kraken2'.

---" at this command qiime moshpit classify-kraken2
--i-seqs demux.qza
--i-kraken2-db /projects/microbiome/biological-reference-data/2023.06.05-k2-plus-pf-.........."

[Nicholas_Bokulich]

It sounds like you have not installed the correct QIIME 2 distribution or you have not activated your environment. Please see the installation instructions for q2-shotgun on qiime2.org

Good luck!

[Ktalaat55 (Kareem Ismail)]

Thanks i will check the link

[Ktalaat55 (Kareem Ismail)]

hello,
I have installed qiime2 using !git clone GitHub - Gibbons-Lab/isb_course_2023: Materials and presentation for the 2023 ISB Microbiome course. materials i am following this link for shotgun installation QIIME 2 Library and still getting an error /bin/bash: line 1: conda: command not found. I am a little confused on how to properly install qiime2 for shotgun analysis on google colab

[Nicholas_Bokulich]

Hi @Ktalaat55 ,
The course that you linked to is installing an older release of QIIME 2, and does not install the necessary plugins for shotgun analysis. You must follow the instructions on qiime2.org to install the q2-shotgun distribution, as mentioned above.

Colab will not have enough resources for analyzing shotgun data, as only limited resources are provided in each instance.