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.

Please work through the documentation and add your comments on the bottom of this page, or email comments to support@cyverse.org. Thank you.

Rationale and Background

LASTDB prepares the necessary nucleotide databases necessary for the LAST (Local Alignment Search Tool) program (Kielbasa et. al., 2011; Genome Research).

INPUT

  • Genome file: Path to the subject genome (or other nucleotide sequence) for which a database will be made. Nucleotide sequences in fasta format. File extensions can be FA, FASTA, FNA, or FAA.
  • Database ID: Name of the database generated, as well as prefix given to all database associated files.
  • Nucleotides to index: This tells the program which nucleotides to index. Default is 2, which means that every other nucleotide is indexed. For comparison, BLAT indexes every 11th position, whereas MegaBLAST indexes every 5th. Increasing this number will decrease memory and disk usage as well as overall run time, but will reduce sensitivity in the LAST alignment step.

Test Run

All files are located in the Community Data directory of the CyVerse Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > LAST > LASTDB (/iplant/home/shared/iplantcollaborative/example_data/LASTDB)

Mandatory arguments: 

  • Genome file: Gmax_genome_chr1.fasta
  • Database ID: Gmax_Chr1_DB
  • Nucleotides to index: 2

 

This Test Run will take approximately 5-10 minutes to complete in the DE. An analysis folder will be created containing all the files generated by LASTDB. There should be seven files total as well as the log folder. All seven database files are necessary for LAST alignment to search properly.