Starting with something like this would be good to get an overall picture of the workflow: Article Metagenomics - A guide from sampling to data analysis

Article An Introduction to the Analysis of Shotgun Metagenomic Data

Then, starting with something like this: https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html or https://bioinformatics.ca/workshops/2018-analysis-of-metagenomic-data/ would be very helpful.

Google it. Everything is there.

Thank you very much Dr. Bazartseren Boldgiv for your help!

Thanks Dr. Abhijeet Singh for your suggestion.

First, you need to find sequencing company and make decision about the type of sequencing (MiSeq or Nanopore). After that, you know that type of raw data you have. Next you chose software for the analysis. Most popular packages are QIIME and Mothur.

Best,

SSS

You can start from sending samples to sequencing either 16S rRNA or whole genome sequencing and once you have fasta files and contigs files with you can can start with two pipelines 1. QIIME 2. MOTHUR. and do the analysis.

Thanks Dr. Sergei Shalygin for your suggestions.

Thanks Mr. Jagdish Parihar for your suggestion.

You can look for tutorial in EBI metagenomics, if you want to analyse a sample data try MG-RAST server or Kaiju server. You may try Galaxy server it has numerous tools and pipeline including tutorials with datasets. Additionally read about sequencing platforms and sequencing chemistry, NGS file types , it will help you a lot. Feel free to contact me in case you need help.

Best Wishes

Pankaj

Thanks a lot dear Pankaj Kumar Singh for the kind suggestions and offering help!