ACDC specifications

Information


Unique identifier OMICS_14377
Name ACDC
Alternative name Automated Contamination Detection and Confidence estimation
Interface Web user interface
Restrictions to use None
Input data A genome assembly.
Input format FASTA
Programming languages C++
License MIT License
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Markus Lux

Information


Unique identifier OMICS_14377
Name ACDC
Alternative name Automated Contamination Detection and Confidence estimation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A genome assembly.
Input format FASTA
Operating system Unix/Linux
Programming languages C++
License MIT License
Computer skills Advanced
Stability Stable
Requirements
C++ compiler, CMake, Boost C++
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Markus Lux

Publication for Automated Contamination Detection and Confidence estimation

ACDC citation

library_books

Genomic Variation and Evolution of Vibrio parahaemolyticus ST36 over the Course of a Transcontinental Epidemic Expansion

2017
MBio
PMCID: 5686534
PMID: 29138301
DOI: 10.1128/mBio.01425-17

[…] Before running the pangenome analysis, contamination in the genomes was assessed with acdc (). Genomes with unusual gene content or genome size identified during the pangenome analysis and suspected of possible contamination were analyzed to identify contamination and remove any suspec […]

ACDC institution(s)
Computational Methods for the Analysis of the Diversity and Dynamics of Genomes, Bielefeld University, Bielefeld, Germany; Center for Biotechnology - CeBiTec, Bielefeld University, Bielefeld, Germany; DOE Joint Genome Institute, Walnut Creek, CA, USA; CITEC centre of excellence, Bielefeld University, Bielefeld, Germany; Australian Centre for Ecogenomics, University of Queensland, ST LUCIA, QLD, Brisbane, Australia
ACDC funding source(s)
This contribution has been made possible through the German-Canadian DFG international research training group “Computational Methods for the Analysis of the Diversity and Dynamics of Genomes” (DiDy) GRK 1906/1. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.

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