Primer Design Pipeline for Isolates

A developing primer design pipeline for the detection of isolates within a bacterial synthetic community

This repository contains scripts to annotate genomes, filter sequences, and design primers for detecting isolates in a synthetic bacterial community. The workflow moves from raw assemblies through annotation to targeted primer generation.

Repository Structure & Workflow

• 0_set-up: Environment setup and dependencies
• 1_prokka: Genome annotation using Prokka
• 2_filtering-seqs: Filtering for unique sequences
• 3_designing-primers: Primer design
• 5_get-primers: Collects and validates final primers

Getting Started

1. Clone repo and set up environments and databases (0_set-up)

   • Installations required: BLAST, Prokka (optional), Primer3
   • Set up a BLAST db containing the SynCom genomes

     # need to concatenate all of the genomes to a single file to make the syncom13 db
     cat *.fasta > combined-genomes.fasta
     # use makeblastdb command on the combined-genomes.fasta
     makeblastdb -in /whereever/genomes/are -dbtype nucl -out /whereever/genomes/are/genome-db
     

2. Annotate genomes (you can skip this step if your genomes have already been annotated)

3. Filter sequences

• Follow scripts in 2_filtering-seqs in numerical order, replacing paths and file names as needed.

5. Design primers

• Follow scripts in 3_designing-primers in numerical order, replacing paths and file names as needed.

6. Collect validated primers

• Follow scripts in 5_get-primers in numerical order, replacing paths and file names as needed.

License

Contact

Maintained by Nicole Geerdes (ngeerdes@iastate.edu).