The mWGS-MAG pipeline is based on metagenome-assembled genome method. Firstly, quality control of the raw data was performed by trimmomatic, and megahit was used for metagenomic assembly. Then, the MAG was reconstructed, mainly including alignment between reads and assembled contigs (bamm), abundance calculation of contigs (metabat2), binning (metabat2), MAG quality control (checkm) and prediction of protein-coding genes (prodigal).
For the species genome obtained from the mWGS-MAG pipeline, further functional analysis can be performed by using annotation tools “Microbial genome annotation” and “Biosynthetic gene cluster”.
The steps of mWGS-MAG 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/mWGS-MAG 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/mWGS-MAG Task and click an eye icon to view interactive graphics.