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DUDes specifications


Unique identifier OMICS_11407
Name DUDes
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The DUDes workflow requires three main inputs: a set of reads, references sequences and a taxonomic tree structure.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Bernhard Y. Rerd <>

Publication for DUDes

DUDes in publications

PMCID: 5924777
PMID: 29740407
DOI: 10.3389/fmicb.2018.00749

[…] computing systems. thus a crude categorisation was made dividing workflows into three groups that either process a file in a timeframe of minutes (12 workflows: capsid, clinical pathoscope, dudes, ensembleassembler, facs, kraken, lmat, metavir, metlab, smart, taxonomer and virana), or hours (19 workflows: giant virus finder, gottcha, imsa, megan, mepic, metashot, metavir 2, nbc, […]

PMCID: 5725470
PMID: 29270165
DOI: 10.3389/fmicb.2017.02445

[…] from different bioinformatics tools as outlined by , who published a computational method called metameta that executes and integrates results from six metagenomic analysis tools (clark – ; dudes – ; gottcha – ; kraken – ; kaiju – ; and motus – ). if the rumen microbiome datasets are strengthened to the same level as the human databases, the joint pipeline will generate more sensitive […]

PMCID: 5600177
PMID: 28924496
DOI: 10.7717/peerj.3729

[…] to horizontal gene transfer events and therefore alternative classification algorithms may be more suitable for contaminant detection than pathoscope (; ). other methods such as microbegps and dudes are alternative similarity based taxonomic classification methods developed to better handle organisms not in a reference database and are also suitable alternatives to pathoscope (; ). […]

PMCID: 5037290
PMID: 27729905
DOI: 10.3389/fmicb.2016.01521

[…] )., new bioinformatic pipelines designed to support researchers involved in functional and taxonomic studies of environmental microbial communities have been released like biomas (fosso et al., ), dudes (piro et al., ), or mocat2 (kultima et al., ), among others., since there is an increasing number of complex communities sequenced, improved statistical methodology is needed, especially […]

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DUDes institution(s)
Research Group Bioinformatics (NG4), Robert Koch Institute, Berlin, Germany; CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil; 4-Antibody AG, Basel, Switzerland
DUDes funding source(s)
This work was supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) - Ciência sem Fronteiras [BEX 13472/13-5].

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