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FGP specifications

Information


Unique identifier OMICS_14961
Name FGP
Alternative name FunGene Pipeline
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline James Cole <>

Information


Unique identifier OMICS_14961
Name FGP
Alternative name FunGene Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
RDPTools, HMMER3, Infernal, USEARCH
Maintained Yes

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Maintainer


  • person_outline James Cole <>

Publications for FunGene Pipeline

FGP in publications

 (13)
PMCID: 5730597
PMID: 29242567
DOI: 10.1038/s41598-017-17309-x

[…] with a minimum read q score of 25, sequence length between 240 and 275 bp and no ambiguities as parameters. the assembled amplicon sequences were checked for chimeras using the uchime tool on the fungene pipeline of the rdp website. after assembly and the first chimera check, samples were processed with mothur following the miseq sop,. sequences were aligned to the silva bacterial 16s rrna […]

PMCID: 5705078
PMID: 29182670
DOI: 10.1371/journal.pone.0188223

[…] detected in some samples ()., pmoa reads from the illumina amplicon sequencing were first assembled using the usearch command “fastq_mergepairs” from uparse [] and then further analyzed using the fungene pipeline []. reads shorter than 400 bp were discarded and chimeras were checked and removed with uchime []. sequences were translated to amino acids and compared to the pmoa reference […]

PMCID: 5678694
PMID: 29117259
DOI: 10.1371/journal.pone.0187858

[…] further analysis was performed on qiime platform (qiime 1.9.1) []with a combined sequence file from all the samples. a custom database was constructed by downloading all mcra gene sequences from the fungene pipeline version 8.1[]. otus were generated from the combined sequence file using the (pick_otus.py) script in qiime with uclust otu picking method[], and a cut-off value of 84% was applied […]

PMCID: 5645501
PMID: 29081767
DOI: 10.3389/fmicb.2017.01972

[…] were detected and corrected with framebot (length cutoff = 80 aas), aligned using hmmer3 aligner (with nifh as representative gene) and then clustered by rdp mcclust (90% similarity) in the fungene pipeline at rdp (fungene.cme.msu.edu). the resulting cluster file was converted into an otu table by a rdp cluster file formatter in r (version 3.2.5; https://www.r-project.org/). otus […]

PMCID: 5559484
PMID: 28814720
DOI: 10.1038/s41598-017-07769-6

[…] analysis was done from the a189 primer, using roche 454 flx titaniumtechnology (research and testing laboratories, lubbock, texas). raw sequence data was trimmed of low-quality bases using the fungene pipeline, and reads shorter than 150 base pairs were removed. chimeric sequences were removed using usearch 6.0. amino acid translations of sequences were obtained using framebot, […]


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FGP institution(s)
Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA; Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
FGP funding source(s)
This work was supported by grants from the Office of Science (BER), U.S. Department of Energy, Grant DE-FG02-99ER62848 and Bioenergy Center Grant DE-FC02-07ER64494, Superfund Research Program grant P42 ES004911 from the U. S. National Institute of Environmental Health Sciences, National Research Initiative 2008-35107-04542 from the USDA National Institute of Food and Agriculture and NIH Human Microbiome Project Demonstration Project UH3 DK083993.

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