I'm a bioinformatics student, and we are tasked with assessing bacterial diversity and detecting the abundance of microbes in various environments from shotgun metagenomic sequencing data.
I hope you can help me with the pipeline, tools, and databases that we can use in this case.
A good places to start is to search the forum for concepts you are hoping to learn about.
There is a Qiime 2 Shotgun Metagenomics Distribution tutorial which will be helpful to you in getting started. Please keep in mind that this distribution is an alpha release! We are very interested in feedback and there will likely be some bumps along the way in your analysis. The forum is here to help should you get stuck.
Once you have a feature table you should be able to follow the amplicon tutorials to explore bacterial diversity and differential abundance.
I hope this is helpful to you in getting started! Feel free to reach out when you have more specific questions down the line.