This analysis pipeline is built and maintained by Deng Lab and it is suitable for high-throughput sequencing data analysis, focusing on amplicon sequencing data (16S rRNA, ITS, 18S rRNA and functional genes).

This platform requires manual register. Please send your full name, affiliation and supervisor name to Prof. Ye Deng (yedeng@rcees.ac.cn) for registration.

Galaxy Platform page: https://dmap.denglab.org.cn

Citation: Kai Feng, Zhaojing Zhang, Weiwei Cai, Wenzong Liu, Meiying Xu, Huaqun Yin, Aijie Wang, Zhili He, Ye Deng. Biodiversity and species competition regulate the resilience of microbial biofilm community. Molecular Ecology 26 (2017) 6170-82. DOI:10.1111/mec.14356

This analysis pipeline is built and maintained by Metagenomics for Environmental Microbiology (MEM) (Deng Lab) and it is used to model, analyze and manage the the Molecular Ecological Networks (MENs) for adjacent matrix and Inter-Domain Ecological Networks (IDENs) for bipartite matrix from metagenomic datasets, e.g. GeoChip and Sequencing, and synchronous plant surveys, including Molecular Ecological Network Analysis (MENA) Pipeline and InterDomain Ecological Network Analysis Pipeline (IDENAP).

This platform is registry-open.

Galaxy Platform page: https://inap.denglab.org.cn

Citation: Kai Feng, Xi Peng, Zheng Zhang, Songsong Gu, Qing He, Wenli Shen, Zhujun Wang, Danrui Wang, Qiulong Hu, Yan Li, Shang Wang, Ye Deng. iNAP: an integrated Network Analysis Pipeline for microbiome studies. iMeta. 2022,1:e13. https://doi.org/10.1002/imt2.13

This analysis pipeline is built by Deng Lab. It is used for sequence database management and primer assessment.

Galaxy Platform page: https://ardep.denglab.org.cn

Citation: Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang, Ye Deng*. ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies. International Journal of Environmental Research and Public Health, 2020, 17: 5958. DOI:10.3390/ijerph17165958

This pipeline is used for antibiotic resistance genes (ARGs) analysis based on the Sequence Database for ARGs (SDARG).

Galaxy Platform page: https://arga.denglab.org.cn

Citation: Ziyan Wei, Yueni Wu, Kai Feng, Min Yang, Yu Zhang, Qichao Tu, Jun Wang and Ye Deng*. ARGA, a pipeline for primer evaluation on antibiotic resistance genes. Environment International, 2019, 128: 137-145. https://doi.org/10.1016/j.envint.2019.04.030

This pipeline is used for nitrogen functional gene analysis based on the Sequence Database for NcycFunGen.

Galaxy Platform page: https://ncycfungen.denglab.org.cn

Citation: Zhujun Wang,Kai Feng,Ziyan Wei,Yueni Wu,Kazuo Isobe,Keishi Senoo,Xi Peng,Danrui Wang,Qing He,Xiongfeng Du,Shuzhen Li,Yan Li,Ye Deng*, 2022, Methods in Ecology and Evolution. doi: ttps://doi.org/10.1111/2041-210X.13946

It is used for reconstruct full-length functional(or ribosomal) genes from microbial community short read sequencing data.

Galaxy Platform page: https://remirge.denglab.org.cn