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quandico specifications

Information


Unique identifier OMICS_07419
Name quandico
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.14
Stability Stable
Requirements
ggplot2, perl, strawberry, qcluster, quandico
Maintained Yes

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Documentation


Publication for quandico

quandico in publications

 (2)
PMCID: 5863855
PMID: 29566657
DOI: 10.1186/s12885-018-4229-5

[…] due to varying number of pcr amplicons, sequence variation, or pcr enrichment efficiency. for cnv detection in our pcr-enriched amplicon sequencing data of the 20 genes, we used two algorithms, quandico [] and oncocnv [], specifically developed for cnv analysis of amplicon sequencing data. the cnvs detected with these algorithms were then verified experimentally using the multiplex […]

PMCID: 5620233
PMID: 28978093
DOI: 10.18632/oncotarget.19138

[…] genome analysis toolkit 3.3 [, ]., we used lofreq 2.1.1 pipeline for detection of single nucleotide variants (snvs) and insertions/deletions (indels) variants with default parameters []. we used quandico 1.13 [] for copy number variants (cnvs) detection with the following modification to the default setting: primer length was set to 21 (average primer length of our generead panel); reads […]


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quandico institution(s)
Bioinformatics Assay Design and Analysis, QIAGEN GmbH, Hilden, Germany; Bioinformatics Assay Design and Analysis, QIAGEN Sciences Inc, Frederick MD, USA

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