Program for microsatellite selection and primer design

QDD - version 3

A user-friendly program to select microsatellite markers and design primers from large sequencing projects.

Windows and Linux
Command line and Galaxy server version

Emese Meglécz and Jean-François Martin

Aix-Marseille Université, CNRS, IRD, UMR 7263 – IMBE, Equipe EGE Case 36, 3 Place Victor Hugo, 13331; Marseille Cedex 3, France

Montpellier SupAgro, INRA, CIRAD, IRD, Centre de Biologie et de Gestion des Populations, Campus International de Baillarguet, CS30016, 34988 Montferrier-sur-Lez, France




In microsatellite development, high throughput sequencing has replaced the classical cloning based methods and in this process the first two versions of QDD played an important role by dealing with the essential bio-informatics steps leading from raw sequences to primer design.

The original version of QDD aimed to extract the best (putative) markers from a few Megabases (5-500 Mb) of 454 pyrosequences, since back in 2010 only this sequencing platform provided sufficiently long reads (300-500 bases). QDD1 treated all bioinformatics steps from raw sequences all the way to obtaining PCR primers: sorting sequences by tag, removing adapters/vectors, detection of microsatellites, detection of redundancy/possible mobile element association, and primer design.

QDD2 relaxed the primer design conditions, and let the users choose among more markers based mainly on the target region pattern.

QDD3 (current version) aims to improve primer design in the following ways

QDD3 is currently available in two different forms:

QDD scripts can be either downloaded directly, and they should be installed together with all the third party programs, or they can be downloaded pre-installed (as well as the third party programs) into a ready to use virtual machine. In both case, they can be run from Galaxy or from a command line.

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General Description

QDD is composed of four parts. Each of them can be run separately, or all at once in a pipeline

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Main output file(s): Primer table

The main output files are the primer tables produced by pipe3 and completed by pipe4. They are named xxx_pipe[3,4]_primers.tabular in command line version and Table with primers in Galaxy.

Each line corresponds to a primer pair and there are several primer pairs designed for each sequences.

For each primer pair information is given on

Pipe4 completes the output table of pipe3 with

Take your time to understand the information in the different columns in this table, since it helps you to choose markers and primer pairs out of the many designed. (see detailed description of the columns in Output files section)

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How to choose primers from the primer table.

The following suggestions are based on our lab tests (Meglécz et al submitted) or simply on common sense. The title of the column in the output file relevant for each selection criterion is indicated in capital letters.

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Disclaimer: The software on this page is free to download and use, and thus comes with no warranty of any kind. While it hasn't caused us any problem, the current version of QDD is still considered as a beta version and you are responsible for any damages or loss of data you may sustain while using this software.

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Correspondence, comments and bug reports about this program should be addressed to Emese Meglécz