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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

 (7)
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

[…] 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

[…] nscripts 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 with op […]

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

[…] 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 below a rea […]

call_split

Analysis of the leaf transcriptome of Musa acuminata during interaction with Mycosphaerella musicola: gene assembly, annotation and marker development

2013
BMC Genomics
PMCID: 3635893
PMID: 23379821
DOI: 10.1186/1471-2164-14-78
call_split See protocol

[…] K-mers in sequence data was obtained using the software Nesoni version 0.89 (Victorian Bioinformatics Consortium), with sequence groups with distinctive K-mer frequencies clustered accordingly using WcdEST version 0.6.3 []. Sequence assembly of cluster group members into contigs and singletons was performed using the assembly program MIRA version 3.1 [], with 454 technology-specific and expected […]

call_split

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
call_split See protocol

[…] n be quantified using the well-known distance measure called d2. It was first proposed by , and later it is widely accepted and embedded into the established EST clustering tools such as d2_cluster , wcd and PEACE . We choose the same d2 as the distance metric for our local feature, due to its reliability and acceptability. The use of this distance measure is also in-line with our main goal, whic […]

library_books

PEACE: Parallel Environment for Assembly and Clustering of Gene Expression

2010
Nucleic Acids Res
PMCID: 2896108
PMID: 20522511
DOI: 10.1093/nar/gkq470

[…] tools to real Sanger data, we used the Human Benchmark data set used to test EasyCluster () and the A076941 Arabidopsis thaliana data set used to test WCD () (). We notice mixed results, with PEACE, WCD and TGICL showing comparable similarity, PEACE and WCD showing some superiority to TGICL in Type 1 error rate, but with a poorer showing in Type 2 error rate, and with all three tools coming consi […]

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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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