GraftM pipeline

GraftM specifications

Information


Unique identifier OMICS_28496
Name GraftM
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.11.1
Stability Stable
Requirements OrfM v, HMMer v, fxtract, pplacer v, Krona v, MAFFT v, DIAMOND v
Maintained Yes

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Documentation


Maintainer


  • person_outline Gene W. Tyson <>

Additional information


https://github.com/geronimp/graftM/wiki http://geronimp.github.io/graftM/

Publication for GraftM

GraftM citation

2017
PMCID: 5561297

[…] as well as short and low-quality sequences (phred33 ≥ 20) while keeping unpaired reads., taxonomic profiles were obtained from shotgun metagenomic data by extracting 16s rrna gene sequences with graftm v0.10.1 (https://github.com/geronimp/graftm) and mapping them with the 97% clustered greengenes database provided by graftm developers (package 4.39)., functional analyses of the metagenomic […]

GraftM institution(s)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, QLD, Australia
GraftM funding source(s)
Supported by Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research [DE-SC0004632, DE-SC0010580, DE-SC0016440]; Australian Research Council (ARC) Postgraduate Award; ARC Discovery Early Career Researcher Award [DE-160100248]; University of Queensland Vice Chancellor Research Focused Fellowship.

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