Scrimer – designing primers from transcriptome data

With the rise of next-generation sequencing methods it has become increasingly possible to obtain genome-wide sequence data even for non-model species. Such data are often used for the development of single nucleotide polymorphism (SNP) markers, which can subsequently be screened in a larger population sample using a variety of genotyping techniques. Many of these techniques require appropriate locus specific PCR and genotyping primers. Currently there is no publicly available software for the automated design of suitable PCR and genotyping primers from next-generation sequence data.

Here researchers from the Charles University in Prague present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs, and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely-used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash workflow that connects these modules. Even the basic steps are presented, so the workflow can be executed in a step-by-step manner. The use of standard formats throughout the pipeline allows data from various sources to be plugged in, as well as easy inspection of intermediate results with visualization tools of the user’s choice.


Availability – Scrimer is available as the ‘scrimer’ package from the Python Package Index ( and should be installed with the Python pip tool. Scrimer documentation is available at The source of the package and a bug tracker is available at A VirtualBox image of a machine with a fully installed Scrimer package, with dependencies and a sample data set, can be downloaded at

Mořkovský L, Pačes J, Rídl J, Reifová R. (2015) Scrimer: designing primers from transcriptome data. Mol Ecol Resour [Epub ahead of print]. [abstract]

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