The 16S rRNA pipeline is based on Qiime2, and mainly includes species diversity study, differential flora study and differential function study.
Species diversity study
Based on the representative sequences and feature abundance profile, a phylogenetic tree is constructed to further analyze the alpha diversity within the group and beta diversity between the groups.
Differential flora study
Based on the representative sequences and feature abundance profile, the flora abundance profile is firstly obtained through species annotation. Then, Wilcoxon rank sum test and LEfSe are used for identifying the differential flora and biomarker between the groups.
Differential function study
Based on the representative sequences and feature abundance profile, the functional abundance profiles of Enzyme Commission number, KEGG ORTHOLOGY and pathway are firstly obtained through function prediction. Then, LEfSe is used for identifying the differential function between the groups.
The steps of 16S rRNA pipeline (for more information, please refer to user manual)
1、Register an account. If you don’t have an iMAC account, please click here to register your account.
2、Login. If you already have an iMAC account, please click login in the navigation bar.
3、Upload data. Download the FTP client software FileZilla, and log in sftp://fms.biosino.org:44399 using the registered user name and password. Then, upload your data through FileZilla and browse them in user center/Data module.
4、Create new task. In the user center/Task List/16S rRNA Task, click “New Task” to create a 16S rRNA pipeline task. Then, adjust the default parameters according to your requirement and submit.
5、Download results. After the task is finished, you can download the results in the user center/Task List/16S rRNA Task and click an eye icon to view interactive graphics.