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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 citations

 (18)
library_books

The effect of bio irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene

2018
PLoS One
PMCID: 5800672
PMID: 29408934
DOI: 10.1371/journal.pone.0192391

[…] w.bioinformatics.babraham.ac.uk/projects/fastqc/) [].We eliminated potential chimeras using the USEARCH package [,]. Non-target reads (non-nosZ reads) were filtered out using FrameBot included in the Fungene pipeline (http://fungene.cme.msu.edu/). We retrieved a reference set of nosZ protein sequences of 163 different species with high scores (>919) and 98% coverage with a hidden Markov model (HMM […]

library_books

A Coxiella mutualist symbiont is essential to the development of Rhipicephalus microplus

2017
Sci Rep
PMCID: 5730597
PMID: 29242567
DOI: 10.1038/s41598-017-17309-x

[…] seq 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 ref […]

library_books

Diversity and potential activity of methanotrophs in high methane emitting permafrost thaw ponds

2017
PLoS One
PMCID: 5705078
PMID: 29182670
DOI: 10.1371/journal.pone.0188223

[…] 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 sequence […]

library_books

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period

2017
PLoS One
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 fo […]

call_split

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia

2017
Front Microbiol
PMCID: 5645501
PMID: 29081767
DOI: 10.3389/fmicb.2017.01972
call_split See protocol

[…] ameshifts 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 were as […]

library_books

Community structure of rare methanogenic archaea: insight from a single functional group

2017
PMCID: 5812523
PMID: 29029047
DOI: 10.1093/femsec/fix126

[…] quality scores less than 25. We also discarded sequences shorter than 300 or longer than 600 nucleotides. The sequences were then aligned against pre-aligned mcrA sequences which were provided by the FunGene Pipeline (http://fungene.cme.msu.edu/) (Fish et al.). After removing the bad alignments, the remaining sequences were subjected to chimera detection with the UCHIME algorithm (Edgar et al.) in […]

Citations

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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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