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
Hi @Ktalaat55 ,
DId you check the tutorials page of the forum? Please see here:
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
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
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
Thanks i will check the link
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
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.
An off-topic reply has been split into a new topic: installing q2-shotgun distribution on windows
Please keep replies on-topic in the future.