The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g., 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').

Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact support@cyverse.org.

In critical cases, please report your concern to the CyVerse Ask forum or to support@cyverse.org. Thank you for your patience.

The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.

Please work through the tutorial and add your comments on the bottom of this page, or send comments per email to upendra@cyverse.org. Thank you.

Rationale and background: 

 MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8

Prerequisites

  1. A CyVerse account. (Register for an CyVerse account here - user.cyverse.org.)

  2. Input: Select one of the following. Accepted file formats include fasta (.fasta.fa.fna) or fastq (.fastq.fq) or gzip files (with .gz extensions) and bzip2 files (with .bz2 extensions)

    1. Single End Reads
    2. Interleaved Paired End Reads
    3. Paired End Reads (Read 1) - If you selected this option you should select the below option as well
    4. Paired End Reads (Read 2)
  3. Output options
    1. Output folder Name: Name of the output folder
    2. Minimum contig length: Default is 200bp
  4. Advanced Parameters (Optional)
    1. Presets parameters: The available options include meta, meta-sensitive, meta-large, bulk and single-cell

Test/sample data:

Use the following inputs/outputs and parameters for testing Megahit-1.0.6. The test data is available here: /iplant/home/shared/iplantcollaborative/example_data/megahit

  1. Input

    1. Paired End Reads (Read 1) - SRR341725_1.fastq.gz

    2. Paired End Reads (Read 2) - SRR341725_2.fastq.gz
  2. Output

    1. Output File Name: megahit_out
      1. intermediate_contigs folder
      2. final.contigs.fa
      3. opts.txt
  3. Advanced Parameters (Optional): None


More information about Megahit-0.6.1 can be found at Megahit

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