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CnD specifications

Information


Unique identifier OMICS_00338
Name CnD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained No

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Publication for CnD

CnD in publications

 (6)
PMCID: 4968449
PMID: 27480531
DOI: 10.1186/s13059-016-1024-y

[…] were estimated for all variants. sift predicts amino acid substitution effects on protein function and classifies variants as being either tolerated or deleterious., a combination of breakdancer [], cnd [] and lumpy [] were used to identify larger structural deletions/losses (greater than 100 bp). breakdancer identifies large deletions using deviations from the expected mate pair distance […]

PMCID: 4445795
PMID: 26016481
DOI: 10.1186/s12864-015-1592-3

[…] and integration using multiple sv discovery algorithms, producing a single consensus sv callset. the svmerge pipeline was run with 4 calling algorithms: breakdancer 1.0, pindel 0.2.4q, secluster and cnd [-]. after merging the results of these 4 callers into a single consensus callset, the velvet genome assembler was used to attempt breakpoint assembly for all svs in the callset []., deleterious […]

PMCID: 3604020
PMID: 23527109
DOI: 10.1371/journal.pone.0059128

[…] of the existing cnv detection methods to the best of the authors’ knowledge. rsw-seq was excluded because of no publicly available codes. cnanorm was not available when we started our study. cnd and cnaseg were excluded because of stability issue. from the same dataset, there were issues getting the code to fully perform to our expectations. our study focused on the method with doc […]

PMCID: 3491372
PMID: 22916792
DOI: 10.1186/gb-2012-13-8-r72

[…] patterns (figure andtable ) as described in yalcin et al. [,]. to identify structural variants from basic paired-end mapping patterns and changes in mapped read depth, we used breakdancer [], cnd [], secluster (unpublished) and retroseq [] in the svmerge [] pipeline (database of genomic variants archive accession estd200). using the de novo assembly pipeline in svmerge with reads […]

PMCID: 3446317
PMID: 22703977
DOI: 10.1186/gb-2012-13-6-r45

[…] ., structural variant (sv) deletions in all inbred strains were detected using three methods: split-read mapping (pindel []), mate-pair analysis (breakdancer, release-0.0.1r61 []), and read-depth (cnd []). following merger of these calls into a non-redundant set, computational validation by local assembly and breakpoint refinement was performed. details of the complete pipeline, svmerge, […]


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CnD institution(s)
Wellcome Trust Sanger Institute, Hinxton, UK

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