QDD, a free software to analyze microsatellites from NGS data

[martinjf]

We are happy to announce the official release of QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects.

QDD is designed to treat all bioinformatics steps from raw sequences till obtaining PCR primers: Sorting sequences by tag, removing adapters/vectors,
detection of microsatellites, detection of redundancy/possible mobile element association, selection of sequences with target microsatellites and sufficiently long nanosatellite-free flanking regions, and primer design.



The program can be run both under Linux and Windows in an a easy to use command line option, the windows version is supported by a Graphical User Interface.

executables and a manual are available at:

http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html

more details and the corresponding article in Bioinformatics can be found at:
http://bioinformatics.oxfordjournals...stract/btp670?



Jean-François Martin
Centre de Biologie et Gestion des Populations (CBGP)
Montpellier SupAgro
Campus International de Baillarguet
CS 30 016
34 988 Montferrier sur Lez Cedex

tél: 00 33 (0)4 99 62 33 20
fax : 00 33 (0)4 99 62 33 45
mail: [email protected]

[Thimble_12]

QDD help

Hello,

We recently came across QDD while looking for tools to develop microsat markers in a pathogen we study. At present, we have a reference strain that has been sequenced and assembled using PacBio and several other isolates that have been sequenced and assembled both with PacBio and Illumina sequencing. We’re finding QDD really useful to identify good candidate microsat regions in the reference strain. To save both time and money, we were thinking it might be nice to take some of the candidate markers and run them in silica with the other isolates to look and see whether there is variation at the sites, before we start purchasing probes. Is there a way QDD can be run that will enable us to find variation at candidate marker sites? Ideally we’d like more than 2 alleles at the sites, so we’re hoping QDD can help us.

[martinjf]

Dear user
first I would like to make sure that you are using the lastest version of QDD that is QDD3 available at http://net.imbe.fr/~emeglecz/qdd.html
It explicitly takes contigs into account a a couple of improvements compared to previous versions.

As far as I understand your question you would like to develop markers for which you have polymorphism on the basis of sequences you already have ? If so yes you can do it. Just put together in the input file (step 1) all the sequences together (I would recommend using a prefix in the sequence name for each strain) and run the pipeline. In step 2, QDD will concatenate what are recognized as alleles for each given locus (there is a number of mutations threshold to do that) and provide consensus sequence using IUPAC codes. This allows focusing your primer design on those consensus sequences for which the polymorphism is ensured.

I hope it answers your question.
Regards,
Jean-Francois

[Thimble_12]

Hello

Yes, I think we're using QDD3 as we downloaded recently.

That's great. Yes, you have grasped our question there and your reply makes sense to me, although I am not a bioinformatician, I shall pass your answer on to them and see how it goes. Thank you!

C