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DNA Subway

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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).


.. toctree::
        :maxdepth: 2

        Tutorial home <self>
        DNA Subway Basics and Logging in to Subway <step1.rst>
        Accessing Saved Private and Public DNA Subway Projects <step2.rst>
        Walkthrough of DNA Subway Red Line - Genome Annotation <step3.rst>
        Walkthrough of DNA Subway Yellow Line - Sequence Detection <step4.rst>
        Walkthrough of DNA Subway Blue Line - DNA Barcoding and Phylogenetics <step5.rst>
        Walkthrough of DNA Subway Green Line: Kallisto/Sleuth - RNA-Seq <step7.rst>
        Walkthrough of DNA Subway Purple Line (Beta) <step8.rst>

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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