{"id":31942267,"url":"https://github.com/irahorecka/sequencing-primer-generator","last_synced_at":"2026-07-22T04:05:59.918Z","repository":{"id":40975898,"uuid":"198116524","full_name":"irahorecka/sequencing-primer-generator","owner":"irahorecka","description":"A tool to batch-generate optimal DNA primers for Sanger sequencing. 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The output .xlsx file is directly compatible for bulk input into IDT Oligo Entry.\n\n## Introduction\nIn this repository, there are two files: Primerwalk_GUI.py and Primerwalk.py. Primerwalk_GUI.py is a front end desktop application that communicates with the backend Primerwalk.py python file. This repository would be most helpful for molecular biologist who frequently conduct full plasmid sequencing. \u003cbr\u003e\n\nThere are licensed softwares that provide primer synthesis capabilities, but none that can synthesize appropriate forward and reverse primers in batch. The exported files of Primerwalk.py is compatible for single tube ordering and 96-well plate ordering from IDT (idtdna.com).\u003cbr\u003e\n\nSingle tube ordering form: https://www.idtdna.com/site/order/oligoentry \u003cbr\u003e\n96-well plate ordering form: https://www.idtdna.com/site/order/plate/index/pico/5647\n\u003cbr\u003e\n\n## How to use\n\n### Python version and installing required packages\nPython version: **3.7.3**\u003cbr\u003e\nInstalling packages:\u003cbr\u003e\n```$ pip install -r requirements.txt```\n\n### Starting application\n\n```$ python Primerwalk_GUI.py```\n\n### Input file formatting\n\nEnsure that Primerwalk_GUI.py, Primerwalk.py, sequence_file.csv are stored in the same directory. \n\nPlease adhere precisely to the headers in *sequence_file.csv*, outlined below (note: the headers are case sensitive - please adhere as exactly as listed): \u003cbr\u003e\n\u003cbr\u003e\n*sequence_file.csv*\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/jCFubfz.png\" alt=\"alt text\"\u003e \u003cbr\u003e\u003cbr\u003e\n\n**Name**: Name of plasmid / DNA sample\u003cbr\u003e\n**Full Sequence**: Full sample DNA sequence (case insensitive)\u003cbr\u003e\n**Primer Walk**: Sequence of DNA to be sequenced (this could equate to Full Sequence, if desired - case insensitive)\u003cbr\u003e\n**BP Gap**: Base pair gap between primers (usually, max is 500 bp before sequence resolution is compromised)\u003cbr\u003e\n**Primer conc. (nM)**: Primer concentration to order (usually 25nM or 100nM) - used for single tube ordering\u003cbr\u003e\n\u003cbr\u003e\n\n### Running Primerwalk_GUI.py on terminal\n\n1) Navigate through your terminal to the directory in which Primerwalk_GUI.py is installed.\u003cbr\u003e\n2) Start ```Primerwalk_GUI.py``` application\u003cbr\u003e\n3) The following desktop application should appear:\u003cbr\u003e\n\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/nKVMKuh.png\" alt=\"alt text\" width=\"500\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\n\n### Choosing Single Tubes:\n\nIf you would like to order single tubes of primers from IDT, click the 'SINGLE TUBES' button on the desktop application. When executed, the desktop application would look like this: \u003cbr\u003e\u003cbr\u003e\n\n\u003cimg src=\"https://i.imgur.com/hZEgnl0.png\" alt=\"alt text\" width=\"500\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\nA new directory with today's date will be created in your main directory (i.e. the directory with your Primerwalk_GUI.py, Primerwalk.py, and sequence_file.csv files). \u003cbr\u003e\nInside the directory, you will find unique .xlsx files for every plasmid you inputted in the 'sequence_file.csv' file. \u003cbr\u003e\u003cbr\u003e\nEach file will have the following naming format: *IDT_Tube_(plasmid name).xlsx*\u003cbr\u003e\nThe .xlsx file will look like this:\u003cbr\u003e\u003cbr\u003e\n\n\u003cimg src=\"https://i.imgur.com/G6BbcAq.png\" alt=\"alt text\"\u003e \u003cbr\u003e\u003cbr\u003e\n\nUpload this file directly to this \u003ca href=https://www.idtdna.com/site/order/oligoentry\u003ewebsite\u003c/a\u003e and perform the following tasks: \u003cbr\u003e\u003cbr\u003e\n*Click on button 'Bulk Input' in center of webpage (blue button)*\u003cbr\u003e\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/ReISAAS.png\" alt=\"alt text\" width=\"600\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\n*Click on button 'Choose File' to upload your .xlsx ordering forms*\u003cbr\u003e\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/m9CKjG8.png\" alt=\"alt text\" width=\"600\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\nAll required fields in the ordering form should automatically fill. Proceed to checkout if satisfied with input.\n\u003cbr\u003e\u003cbr\u003e\n\n### Choosing 96-Well Plate:\n\nIf you would like to order your primers in a 96-well plate, click the '96-WELL PLATE' button on the desktop application. When executed, the desktop application will look like this: \u003cbr\u003e\u003cbr\u003e\n\n\u003cimg src=\"https://i.imgur.com/wI7EtW1.png\" alt=\"alt text\" width=\"500\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\nSimilar to the output file generated when selecting single tubes, a new directory with the name of today's date will be created in your main directory (i.e. the directory with your Primerwalk_GUI.py, Primerwalk.py, and sequence_file.csv files). \u003cbr\u003e\nInside the directory, you will find unique .xlsx files for every plasmid you inputted in the 'sequence_file.csv' file. \u003cbr\u003e\u003cbr\u003e\nEach file will have the following naming format: *IDT_Plate_(plasmid name).xlsx*\u003cbr\u003e\u003cbr\u003e\n\n\u003cimg src=\"https://i.imgur.com/uOAcm3a.png\" alt=\"alt text\"\u003e \u003cbr\u003e\u003cbr\u003e\n\nUpload this file directly to this \u003ca href=https://www.idtdna.com/site/order/plate/index/pico/5647\u003ewebsite\u003c/a\u003e and perform the following tasks: \u003cbr\u003e\u003cbr\u003e\n*Click on button 'Upload Plate(s)' in center of webpage (blue button)*\u003cbr\u003e\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/D0HZNyj.png\" alt=\"alt text\" width=\"800\" height=\"400\"\u003e \u003cbr\u003e\u003cbr\u003e\n*Click on button 'Choose File' to upload your .xlsx ordering forms*\u003cbr\u003e\u003cbr\u003e\n\u003cimg src=\"https://i.imgur.com/XCpuGrv.png\" alt=\"alt text\" width=\"700\" height=\"330\"\u003e \u003cbr\u003e\u003cbr\u003e\nAll required fields in the ordering form should automatically fill. Proceed to checkout if satisfied with input.\u003cbr\u003e\u003cbr\u003e\n\n***Fin***\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Firahorecka%2Fsequencing-primer-generator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Firahorecka%2Fsequencing-primer-generator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Firahorecka%2Fsequencing-primer-generator/lists"}