The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
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.
A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Template file containing a text ASN.1 Submit-block object (suffix .sbt).
- 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)
- Output file name
- Feature Table or Annotation file (suffix .tbl). [Required only if including annotation]
- Structured comment file (suffix .cmt)
- Master Genome Flags
- 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.
- Allows the addition of source qualifiers that will be the same for each submission
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
Template file - template_BP_BS.sbt
- Fasta file - multiple.fsa
- Output file - multiple.sqn
- Optional arguments
- Annotation file - multiple.tbl
- Structured comment file - assembly.cmt
- Organism name - [organism=Helicobacter pylori ABC1] [strain=ABC1] [host=Homo sapiens] [isolation-source=blood]
- Master Genome Flag - n (default)
- Run Discrepency report - checked (default and recommended)
- multiple.sqn - sqn file for submission to WGS
- multiple.val - varification report
- discrep - discrepency report
- 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/