PrimerServer2: a high-throughput primer design and specificity-checking platform

PrimerServer was proposed to design genome-wide specific PCR primers. It uses candidate primers produced by Primer3, uses BLAST and nucleotide thermodynamics to search for possible amplicons and filters out specific primers for each site. By using multiple threads, it runs very fast, ~0.4s per site in our case study for more than 10000 sites.

This repository is based on Python3 and acts as the successor of legacy PrimerServer.

Add these two softwares to your system PATH

• Samtools (>=1.9).
• NCBI BLAST+ (>=2.2.18)

$ pip3 install primerserver2

$ git clone https://github.com/billzt/PrimerServer2.git
$ cd PrimerServer2
$ python3 setup.py install

** (if installed from pip,) tests/query_design_multiple and tests/example.fa can be obtained from this github repository.

** full mode: design primers and check specificity
$ primertool full tests/query_design_multiple tests/example.fa

** design mode: design primers only
$ primertool design tests/query_design_multiple tests/example.fa

** check mode: check specificity only
$ primertool check tests/query_check_multiple tests/example.fa

Please refer to the wiki.