Primer3 is a program for designing PCR primers. Primer3 can also design hybridization probes and sequencing primers.

References:

• Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M and Rozen SG. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012 Aug 1;40(15):e115
• Koressaar T and Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics 2007;23(10):1289-1291.
• Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R and Remm M. Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics 2018;34(11):1937-1938.

• Primer3 Main Site

• Module Name: primer3 (see the modules page for more information)
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load primer3

Following the Primer3 manual's example, create the file example with the following contents:

SEQUENCE_ID=example
SEQUENCE_TEMPLATE=GTAGTCAGTAGACNATGACNACTGACGATGCAGACNACACACACACACACAGCACACAGGTATTAGTGGGCCATTCGATCCCGACCCAAATCGATAGCTACGATGACG
SEQUENCE_TARGET=37,21
PRIMER_TASK=generic
PRIMER_PICK_LEFT_PRIMER=1
PRIMER_PICK_INTERNAL_OLIGO=1
PRIMER_PICK_RIGHT_PRIMER=1
PRIMER_OPT_SIZE=18
PRIMER_MIN_SIZE=15
PRIMER_MAX_SIZE=21
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-100
P3_FILE_FLAG=1
SEQUENCE_INTERNAL_EXCLUDED_REGION=37,21
PRIMER_EXPLAIN_FLAG=1
=

Then run primer3 and show the output files:

[user@cn3144 ~]$ primer3_core < example 

[user@cn3144 ~]$ ls
example
example.for
example.int
example.rev

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. primer3.sh). For example:

#!/bin/bash
set -e
module load primer3
primer3_core < example

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] primer3.sh

Create a swarmfile (e.g. primer3.swarm). For example:

primer3_core < seq1
primer3_core < seq2
primer3_core < seq3

Submit this job using the swarm command.

swarm -f primer3.swarm [-g #] [-t #] --module primer3