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Protocols

ProDeGe specifications

Information


Unique identifier OMICS_27693
Name ProDeGe
Alternative name Protocol for fully automated Decontamination of Genomes
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Maintained No

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Publication for Protocol for fully automated Decontamination of Genomes

ProDeGe citations

 (13)
library_books

Deciphering the Human Virome with Single Virus Genomics and Metagenomics

2018
Viruses
PMCID: 5869506
PMID: 29509721
DOI: 10.3390/v10030113

[…] ontigs matching to human DNA or common bacterial contaminants in single-cell genomics and sequencing [,] were removed from the analyses. Contamination screening was done by using a combination of the ProDeGe program and a comparison with the database nr/nt using standalone BLAST version 2.2.31+. Short contigs from a previous salivary survey [] (maximum length = 349 pb) were reassembled using SPAde […]

library_books

Metabolic capability and in situ activity of microorganisms in an oil reservoir

2018
Microbiome
PMCID: 5756336
PMID: 29304850
DOI: 10.1186/s40168-017-0392-1

[…] ere mapped back to the contigs file, and the resulting bam files were used as input into GroopM with default parameters (v0.3.4) []. De-contamination of retrieved genome bins (GBs) was carried out in ProDeGe []. Bonafide GBs were uploaded to RAST [] for annotation. All GBs were checked for completeness and contamination using checkM v1.0.5 []. […]

library_books

Benefits of Genomic Insights and CRISPR Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems

2017
Front Microbiol
PMCID: 5654357
PMID: 29097994
DOI: 10.3389/fmicb.2017.02036

[…] s whereas MetaBAT clusters contigs iteratively by modified K-methods algorithm. Bins of pathogen-related species from the two binning tools were compared and assessed with CheckM (Parks et al., ) and ProDeGe (Tennessen et al., ), followed by manual curation. The curated bins with ≥90% completeness and ≥15-fold coverage were finalized as draft genomes. Details of each step in the pipeline had been […]

library_books

Single virus genomics reveals hidden cosmopolitan and abundant viruses

2017
Nat Commun
PMCID: 5490008
PMID: 28643787
DOI: 10.1038/ncomms15892

[…] Contigs <1,000 bp and contigs matching to human DNA or common bacterial contaminants in SCGs and sequencing were removed from the analyses. Contamination screening was done by using a combination of ProDeGe program and a comparison with the database nr/nt using the stand alone BLAST version 2.2.31+. Finally, prediction of open reading frames (ORFs) from the curated viral genomes and genome annota […]

library_books

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

2017
PeerJ
PMCID: 5385130
PMID: 28396823
DOI: 10.7717/peerj.3134

[…] sequences) were assembled using SPAdes v3.5.0 () with options –k: 21,33,55,77, --careful –pe1-12 and default parameters. Contaminating contigs in the assembly were screened and removed using the JGI ProDeGe web portal v2.0 (https://prodege.jgi-psf.org/) on April 10, 2015, using default parameters with the following taxonomy specified: “Bacteria; Firmicutes; Clostridia” (). Contigs remaining follo […]

library_books

Draft Genome Sequences of Two Magnetotactic Bacteria, Magnetospirillum moscoviense BB 1 and Magnetospirillum marisnigri SP 1

2016
Genome Announc
PMCID: 4982287
PMID: 27516508
DOI: 10.1128/genomeA.00814-16

[…] d genome coverage were obtained from M. moscoviense BB-1 and M. marisnigri SP-1, respectively. Genome assembly was performed using SPAdes version 3.1.0 (). The resulting contigs were submitted to the ProDeGe website () for automatic decontamination. Finally, the assembled sequences were automatically annotated using the Prokaryotic Genome Annotation Pipeline (PGAP) provided by the National Center […]

Citations

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ProDeGe institution(s)
Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA; Department of Biology and Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA
ProDeGe funding source(s)
Supported by the Office of Science of the US Department of Energy under Contract No. DEAC02-05CH11231; the NSF Microbial Systems Biology grant IOS-0958245 and DOE Plant Feedstocks grant DOESC0010423; the NIH Training Grant T32 GM07092-34; the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (in part via Grant GBMF3030).

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