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WCD specifications

Information


Unique identifier OMICS_24177
Name WCD
Alternative name wcdest
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data a set of DNA sequences.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 0.6.3
Stability No
Maintained No

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Publication for wcdest

WCD citations

 (4)
library_books

Development of EST based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping

2014
BMC Genomics
PMCID: 4265408
PMID: 25442170
DOI: 10.1186/1471-2164-15-1046

[…] [] was used as the mapping population to map all polymorphic markers., the ests of g. hirsutum and g. barbadense downloaded from ncbi (http://www.ncbi.nlm.nih.gov/) were clustered using the wcd program []. all of the clusters were then imported into haplosnper (http://www.bioinformatics.nl/tools/haplosnper/) to identify snps between g. hirsutum and g. barbadense with default parameters. […]

library_books

Construction of a Public CHO Cell Line Transcript Database Using Versatile Bioinformatics Analysis Pipelines

2014
PLoS One
PMCID: 3888431
PMID: 24427317
DOI: 10.1371/journal.pone.0085568

[…] with an ungapped alignment covering at least 90% of the complete length were removed from the set since they are included in a longer sequence. the remaining transcripts were clustered using wcd with default parameters., a re-assembly of the transcripts from the individual assemblies was performed in the third step using cap3 . the assembly was performed for each cluster separately […]

library_books

A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

2013
Genome Biol
PMCID: 4054090
PMID: 23425577
DOI: 10.1186/gb-2013-14-2-r16

[…] of high quality. all individual sanger sequences are available via the newtomics repository [,]., base calling for sanger reads (48,537) was performed by phred. primary clustering was done by wcd [], assembly by cap3 []. the de novo assembly yielded 26,594 unique transcripts. illumina raw read quality was determined using fastqc quality control tool []., illumina sequencing reads […]

library_books

A Hybrid Distance Measure for Clustering Expressed Sequence Tags Originating from the Same Gene Family

2012
PLoS One
PMCID: 3469558
PMID: 23071763
DOI: 10.1371/journal.pone.0047216

[…] are similar. it implies that ests that are overlapping with each other to a certain extent (subsequence length in this case), can be grouped into the same cluster. hazelhurst et al. introduced the wcd tool to cluster ests. it is a clustering method similar to d2_cluster. in fact, both methods apply the same distance measure and also implement the windowing strategy. the key differences […]


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WCD institution(s)
Wits Bioinformatics, University of the Witwatersrand, Johannesburg, Wits, South Africa; South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa; Universität Bielefeld, AG Genominformatik, Technische Fakultät, Bielefeld, Germany
WCD funding source(s)
Supported by the South African National Bioinformatics Network, South African Medical Research Council, South African National Research Foundation (GUN2069114), German Federal Ministry of Education and Research and the Alexander von Humboldt Foundation.

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