On this page you can find descriptions of the methods we use and data we return for various standard analysis workflows. For custom analyses, please contact us at asubioinformatics@asu.edu.
(This page is still incomplete! Thank you for your understanding.)
Differential Gene Expression
- Example Folder Structure
- Sequence Processing and Alignment
- Differential Gene Expression
- Functional Enrichment
Shotgun Metagenomics
- Trim and Filter Reads
- Assembly-Free Taxonomic Classification with KRAKEN
- Assembly-Free Taxonomic and Functional Classification with HUMAnN
- Metagenome Assembly and Annotation
- Functional Genomic Potential Profiling
- Binning for MAG Identification
Shotgun Metatranscriptomics
- Trim and Filter Reads
- Assembly-Free Taxonomic and Functional Classification with HUMAnN
- Metagenome Assembly and Annotation
- RNA Expression Profiling
- Differential Expression Analysis
Paired Metagenomics and Metatranscriptomics
- Trim and Filter Reads
- Assembly-Free Taxonomic Classification with KRAKEN
- Assembly-Free Taxonomic and Functional Classification with HUMAnN
- Metagenome Assembly and Annotation
- Functional Genomic Potential Profiling
- Binning for MAG Identification
- RNA Expression Profiling
- Differential Expression Analysis
Viral-Enriched Metagenomics
- Trim and Filter Reads
- Assembly-Free Taxonomic Classification with KRAKEN
- Assembly-Free Taxonomic and Functional Classification with HUMAnN
- Metagenome Assembly and Annotation
- Functional Genomic Potential Profiling
- Binning for MAG Identification
- Viral Identification and Classification
Viral-Enriched Metatranscriptomics
- Trim and Filter Reads
- Assembly-Free Taxonomic and Functional Classification with HUMAnN
- Metagenome Assembly and Annotation
- RNA Expression Profiling
- Differential Expression Analysis
- Viral Identification and Classification