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QDD specifications

Information


Unique identifier OMICS_05111
Name QDD
Interface Web user interface
Restrictions to use None
License GNU General Public License version 2.0
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_05111
Name QDD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for QDD

QDD in publications

 (12)
PMCID: 5738816
PMID: 29262842
DOI: 10.1186/s13104-017-3084-9

[…] were trimmed for quality and illumina adapters removed using trimmomatic [] and paired reads aligned using flash []. saula/b-linker sequences [] were removed and consensus sequences created with qdd []. finally suitable microsatellites were identified using misa []. a total of 423 unique sequences were selected for potential primer design, based on a minimum of five tandem repeats […]

PMCID: 5581910
PMID: 28900436
DOI: 10.3389/fpls.2017.01488

[…] using the bowtie aligner (langmead et al., ). second, we evaluated the completeness of the assembly in terms of conserved ortholog content with busco (simão et al., )., for ssrs detection we used qdd v.3.1.2 (meglecz et al., ; meglécz et al., ). we inputted the assembled contigs to qdd3 and screened them for ssrs. our search was restricted to perfect ssrs with a minimum length of 20 bases. […]

PMCID: 5584820
PMID: 28924516
DOI: 10.3732/apps.1700055

[…] perennial kangaroo paw, anigozanthos manglesii (haemodoraceae), and related species., using a personal genome machine (pgm) semiconductor sequencer, ca. 4.03 million sequence reads were generated. qdd pipeline software was used to identify 190,000 microsatellite-containing regions and priming sites. from these, 90 were chosen and screened using pcr, and 15 polymorphic markers identified. […]

PMCID: 5546166
PMID: 28791206
DOI: 10.3732/apps.1700023

[…] san diego, california, usa) to construct a nonenriched genomic dna library following , generating 255,460 paired-end reads 145 ± 3 bp long, which were pair-assembled with pandaseq (). the software qdd with the default settings () was used to identify 3597 microsatellite loci following the three classical steps: (i) ssr detection, (ii) elimination of similar sequences, and (iii) primer design. […]

PMCID: 5238703
PMID: 28101438
DOI: 10.3732/apps.1600113

[…] scripts. a total of 25.34 million cleaned 100-bp paired-end reads were de novo assembled into 121,556 contigs (n50 = 906 bp) using trinity version 2.1.1 () with default parameters., the software qdd version 3.1 () was used to search ssr motifs containing two to six nucleotides with the minimum number of repeats as follows: six for dinucleotide and five for trinucleotide, tetranucleotide, […]


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QDD institution(s)
Aix-Marseille Université, CNRS, IRD, Univ Avignon, UMR 7263 - IMBE, Equipe EGE, Centre Saint-Charles, Marseille, France

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