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Data Analysis Pipelines

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Data Analysis Pipelines

ANNOUNCEMENT: Due to a server issue, the Sequence Analysis Pipeline had to be reinstalled.  It is now working, but all previous accounts have been deleted.  If you need access to the pipeline, email to request an account.


NOTICE: Combined data files will be stored for a period of time, but will be deleted after one year. All of the “raw” data will remain on the pipeline for 5 years and then will be archived to a storage server.

Please contact our maintainer ( if you have any questions.


Microarray Data Manager - This pipeline can be used to upload raw microarray data, process the data (normalization, quality filtering, designate signal cutoffs), and analyze the data.  Other types of data can also be used in the pipeline (amplicon sequencing data).

To access this pipeline, please send an email to requesting an account.  Include a short explanation of why you want use the pipelines and allow 24 hours for account setup.

GeoChip Design Pipeline - This pipeline was developed to comprehensively analyze microbial functional genes for the design of Functional Gene Microarrays (FGAs).The program contains multiple modules to download gene sequences, remove low-homology sequences, design oligonucleotide probes, check probe specificity, output selected oligonucleotide probes, and finally store data in local databases. 

This pipeline is restricted to trained users.

Molecular Ecological Network Analysis - This novel mathematical and bioinformatics framework was developed to construct ecological association networks, referred to as molecular ecological networks (MENs), through Random Matrix Theory (RMT)-based methods. This approach allows automatic definition of the network and is robust to noise, thus providing an excellent solution to several common issues associated with high-throughput metagenomics data analysis.

Request access to this pipeline HERE.

Sequencing Analysis Pipeline - This pipeline is used to process raw amplicon sequencing data and raw data can uploaded and used to remove sequences from controls and artifacts, sort, trim, and combine sequences, convert sequences to FASTA format, and generate OTU tables.

ASAP Sequencing Analysis Pipeline - This is an automated pipeline for analysis of amplicon sequence data, including 16S, 18S and ITS. It complements QIIME commands with additional analyses where QIIME performs poorly.

EcoFun-MAP pipeline - This pipeline was developed for automatic analysis of metagenomic sequencing data from an ecological function perspective. Two functional gene databases were utilized, including a protein sequence-based Hidden Markov Model database and a nucleotide sequence-based functional OTU database, both of which were manually curated and specifically tailored for this application. EcoFun-MAP allows profiling of large amounts of raw reads to the functional OTU level, and provides annotation into hierarchical ecological functional categories.

IEG Statistical Analysis Pipeline - This pipeline contains tools for statistical analyses of microbiome data, e.g., taxonomic/phylogenetic diversity metrics, dimension reduction, dissimilarity test, dispersion test, null model test, stochasticity estimation (e.g. normalized stochasticity ratio, NST), quantifying community assembly processes (e.g. the phylogenetic bin-based null model approach, iCAMP), etc..  An account is required to access this pipeline.

ARMAP Shotgun Sequencing Pipeline - ARMAP is an automated pipeline for analysis of shotgun metagenomic sequencing data.  The results include taxonomic and functional classification (SEED, KEGG, COG and GO).