GraftM protocols

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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 in pipeline

2017
PMCID: 5561297
PMID: 28667104
DOI: 10.1128/AEM.00729-17

[…] 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 […]


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GraftM in publications

 (5)
PMCID: 5711877
PMID: 29196695
DOI: 10.1038/s41598-017-17080-z

[…] in a reference 16s rrna gene tree (greengenes may 2013 release) using pplacer v2.6.32. the 16s rrna gene sequence search and phylogenetic placement procedures were performed as implemented in graftm v0.9.5 (https://github.com/geronimp/graftm). a site-by-species operational taxonomic unit (otu) count table was constructed from the graftm output and counts were converted to relative […]

PMCID: 5401914
PMID: 28484436
DOI: 10.3389/fmicb.2017.00682

[…] refined using refinem and finishm as for h. thermophila. the taxonomic identity of each thioreductor genome was confirmed by screening high-quality reads for 16s rrna gene sequence fragments using graftm. putative 16s rrna gene fragments were aligned using the sina web aligner () and inserted into the silva ssu non-redundant database v123.1 using the parsimony insertion tool in arb., […]

PMCID: 5339240
PMID: 28326079
DOI: 10.3389/fmicb.2017.00385

[…] value of 0.97 similarity was empirically confirmed by analyzing the clustering of taxonomical known urec genes. taxonomic assignment of representative sequences of otus was performed using graftm with a likelihood cut-off of 0.75 when using pplacer () for placement of the sequences against a compiled urec gene package. the urec gene package was compiled in graftm with the create […]

PMCID: 5036114
PMID: 27688978
DOI: 10.7717/peerj.2486

[…] read, and compared to the same file before duplicate removal using samtools flagstat., the 16s rrna gene-based taxonomic profiles of the mock community and seawater samples were generated with graftm (http://geronimp.github.io/graftm) using the 16s rrna package (4.06.bleeding_edge_2014_09_17_greengenes_97_otus.gpkg). the pipeline was designed to identify reads encoding 16s rrna genes based […]

PMCID: 4451040
PMID: 26038723
DOI: 10.7717/peerj.968

[…] (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and illumina nextera adaptors were removed using fastx-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). reads were parsed through graftm (https://github.com/geronimp/graftm) version r2439db using the may, 2013 version of the greengenes database 97% otus (operational taxonomic units) as a reference () to identify […]


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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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