The ITS pipeline is based on Qiime2, and mainly includes species diversity study and differential 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.
Based on the representative sequences and feature abundance profile, the 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.
The steps of ITS 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/My Data module.
4、Create new task. In the user center/Task List/ITS Task, click “New Task” to create a ITS 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/ITS Task and click an eye icon to view interactive graphics.