DNA Subway¶
Goal¶
DNA Subway is an educational bioinformatics platform developed by CyVerse. It bundles research-grade bioinformatics tools, high-performance computing, and databases into workflows with an easy-to-use interface. “Riding” DNA Subway lines, students can predict and annotate genes in up to 150kb of DNA (Red Line), identify homologs in sequenced genomes (Yellow Line), identify species using DNA barcodes and phylogenetic trees (Blue Line), examine RNA-Seq datasets for differential transcript abundance (Green Line), and analyze metabarcoding and eDNA samples using QIIME (Purple Line).
- Tutorial home
- DNA Subway Basics and Logging in to Subway
- Accessing Saved Private and Public DNA Subway Projects
- Walkthrough of DNA Subway Red Line - Genome Annotation
- DNA Subway Red Line - Create an Annotation Project with Apollo
- DNA Subway Red Line - Find and Mask Repetitive DNA
- DNA Subway Red Line - Making Gene Predictions
- DNA Subway Red Line - Visualize predicted genes in a Genome Browser
- DNA Subway Red Line - Search Databases using BLAST
- DNA Subway Red Line - Build Gene Models using Apollo
- Walkthrough of DNA Subway Yellow Line - Sequence Detection
- Walkthrough of DNA Subway Blue Line - DNA Barcoding and Phylogenetics
- Walkthrough of DNA Subway Green Line: Kallisto/Sleuth - RNA-Seq
- DNA Subway Green Line: Kallisto/Sleuth - Create an RNA-Seq Project to Examine Differential Abundance
- DNA Subway Green Line: Kallisto/Sleuth - Manage Data and Check Quality with FASTQC
- DNA Subway Green Line: Kallisto/Sleuth - Trim and Filter Reads with FastX Toolkit
- DNA Subway Green Line: Kallisto/Sleuth - Quantify reads with Kallisto
- DNA Subway Green Line: Kallisto/Sleuth- Visualize data using IGV
- DNA Subway Green Line: Kallisto/Sleuth- Visualize data using Sleuth
- Walkthrough of DNA Subway Purple Line (Beta)
- DNA Subway Purple Line - Metadata file and Sequencing Prerequisites
- DNA Subway Purple Line - Create a Microbiome Analysis Project
- DNA Subway Purple Line - Metadata and QC
- DNA Subway Purple Line - Alpha Rarefaction/Clustering Sequences
- DNA Subway Purple Line - Calculate Core Metrics/Alpha and Beta Diversity
- DNA Subway Purple Line - Visualize data with PiCrust and PhyloSeq
Prerequisites¶
Downloads, access, and services¶
In order to complete this tutorial you will need access to the following services/software
| Prerequisite | Preparation/Notes | Link/Download |
|---|---|---|
| CyVerse account | You will need a CyVerse account to complete this exercise | Register |
| DNA Subway Access | DNA Subway access is by request access | Check or request access: CyVerse User Portal |
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