The following steps demonstrate how to design a new script in the Visual view using the Templates panel and Toolkit panel.

  1. Launch SeqNinja. Notice that the Templates panel and Toolkit panel appear on the right. The Welcome screen on the left is a launch point to create or open a script, access items in the Templates panel, or access help and tutorials.
  1. Choose a template from the Welcome screen or the Templates panel. The Visual view will open with a copy of the template loaded as a new script.
To do this… … choose this template:
Create a new, empty SeqNinja (.star) project Blank Script
Add only specified features to a sequence or feature file Add Features
Reset the origin of a circular sequence Change Sequence Origin
Save all files that share a particular naming pattern as a single sequence file or sequence variable Collect Sequences
Combine two or more sequences into a single, new sequence. (e.g., merge contigs into a pseudo-molecule with a linker) Concatenate Sequences
Convert a sequence from one type to another (see our list of supported file formats) Convert File Type
Modify a sequence by inserting new sequence characters Create Insertion
Extract a set of annotated features from a genome and save them as protein or nucleotide sequences Extract Features as Sequences
Map specified annotations from a source sequence to a target sequence Map Features
Create a modified version of a sequence Modify Sequence
Create the reverse complement of one or more sequences in a file Reverse Complement Sequence
Create an output file that contains a filtered set of sequences from the source file Sample Sequences
Save a new, individual output file for each of the sequences in the source file. Split Sequences
Translate one or more DNA sequences into protein Translate
Create a SeqNinja feature table or VCF file using the annotations from a specified sequence file Write Features
  1. Enter the required information. For example, you may be asked to choose a sequence, specify output format and location, or to select a sequence range.
  1. If desired, add additional steps and/or operations to the script using items from the Templates and Toolkit panels. These items can be placed in any order, and some types of operations can be nested inside other operations or steps using drag & drop.
  1. Enter the required information for the newly-added steps.
  1. If desired, save the script as a .star file.
  1. Run the script. SeqNinja will execute the entire script from top to bottom, outputting the results in the file(s) you chose earlier. At the conclusion of the run, the output will be saved in the file(s) and format(s) specified in the script, and the Run Results dialog will appear. This dialog contains links to the folder(s) containing the output file(s).

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