The mWGS-assembly pipeline is based on assembly method. For each sample, this pipeline includes the steps of quality control (KneadData), metagenomic assembly (MEGAHIT), gene prediction (Prodigal or MetaGeneMark). For the genes predicted from each sample, CD-HIT was used to construct the non-redundant gene set. Further, Salmon was used to construct the index of the non-redundant gene set and obtain the gene abundance profile of each sample. Finally, the amino acid sequences of the non-redundant gene set were aligned (DIAMOND blastp) with the sequences of six common functional databases including EGGNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes), UniRef90 (The UniProt Reference Clusters 90), CAZY (Carbohydrate-Active enZYmes Database), VFDB (Virulence Factor Database) and CARD (The Comprehensive Antibiotic Resistance Database), thus obtain the functional abundance profile for each sample.
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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-assembly Task, click “New Task” to create a mWGS-assembly 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-assembly Task and click an eye icon to view interactive graphics.