Template-specific primers design

Question

[Artem Kiselev]

I'm looking for some PCR primers design tool (or pipeline) that can do reference-dependent, template-specific primers design, a good example of this approach is NCBI-Primer-Blast, but it's not possible to run batch-job on NCBI servers, and I can't run this tool local.

I found the JCVI Primer Designer project but it's from one hand is dead, and the other hand is not completed yet.

[Biomonika (Noolean)]

You can design primers with you favorite software and then check for specificity with primersearch from Emboss

[Katie D'Aco]

would primer3 suit your needs? source code is available for you to run locally, although you may need to build a pipeline around it to feed it reference sequence.

[Artem Kiselev]

Of course I know Primer3, but it can't perform primers alignment on chosen genome or mRNA for specificity check.

[Katie D'Aco]

I think primer3 uses a heuristic to estimate genome wide specificity (could be wrong about that). Have you seen PRIMEGENS? Not sure how it works, but it looks like it takes a reference sequence as a parameter.

[Artem Kiselev]

I have completed testing of PRIMEGENS tool (it looked very promising), but unfortinatly web version of this tool work only on test data provided by developer and standalone tool not comleted yet (has limited functionality)...

Answer 1

[Felix Francis]

Try ThermoAlign: A primer design tool for tiled amplicon sequencing (includes multiplexing) using highly specific primers.

Manuscript: http://www.nature.com/articles/srep44437

https://github.com/drmaize/ThermoAlign

Answer 2

[Artem Kiselev]

I founded the tool for this task, PrimerWay, please use:

https://github.com/zoldrax/primer-way