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 anapp reinstated, please contact support@cyverse.org.

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.

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 Though this version of the app works, NCBI recommends the recent version of tbl2asn (ungapped)-25.3 app in DE

Rationale and background: 

Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files using template for submission to GenBank. Additional manual editing is not required before submission.

 Pre-Requisites

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

Mandatory

  1. Template file containing a text ASN.1 Submit-block object (suffix .sbt).
  2. Nucleotide sequence data in FASTA format (suffix .fsa). Can be either a single fasta file (containing a single sequence) or single fasta file (containing multiple sequences) 
  3. Output file name

Optional

  1. Feature Table or Annotation file (suffix .tbl). [Required only if including annotation]
  2. Structured comment file (suffix .cmt)

Parameters

  1. Master Genome Flags 
  2. Runs the Discrepancy Report. Must supply an output file name. Recommended only for annotated genome submissions, complete or WGS. See the Discrepancy Report page for information about its output.
  3. Allows the addition of source qualifiers that will be the same for each submission

Generating the .sqn file for submission

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  • The minimum requirements to generate a Sequin file using tbl2asn are one .sbt file and one or more .fsa files.
  • Tbl2asn will generate a .sqn for every .fsa file in the directory, plus any of the corresponding optional files that may be present. The other files must have the same file name prefix as their corresponding .fsa. (for example helicase.fsa and helicase.tbl).

Test/sample data:


The test data are provided for testing tbl2asn (ungapped)-22.9 in here - /iplant/home/shared/iplantcollaborative/example_data/tbl2asn.sample.data:

Use the following inputs/outputs and parameters for testing tbl2asn (ungapped)-22.9

  1. Mandatory argument

    1. Template file - template_BP_BS.sbt

    2. Fasta file - multiple.fsa
    3. Output file - multiple.sqn
  2. Optional arguments 
    1. Annotation file - multiple.tbl
    2. Structured comment file - assembly.cmt
  3. Parameters
    1. Organism name - [organism=Helicobacter pylori ABC1] [strain=ABC1] [host=Homo sapiens] [isolation-source=blood]
    2. Master Genome Flag - n (default)
    3. Run Discrepency report - checked (default and recommended) 

Output Reports:

  1. multiple.sqn - sqn file for submission to WGS
  2. multiple.val - varification report
  3. discrep - discrepency report
  4. errorsummary.val - Summary file showing the number, severity and type of errors found in all the .val files.

More information about tbl2asn (ungapped)-22.9 can be found at http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

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