Table 4
Open in new tab

MAG taxonomic classification and annotation tools

ToolAccess linkFunctionFirst releaseLast updatedCurrent citationsReference
PhyloSifthttps://github.com/gjospin/PhyloSiftTaxonomic classification2014–438[159]
GTDB-Tkhttps://github.com/ecogenomics/gtdbtkTaxonomic classification20192020129[176]
lastTaxahttps://gitlab.com/jfroula/lasttaxaTaxonomic classification––––
BAT–Taxonomic classification2019–15[168]
MiGAhttp://microbial-genomes.org/Taxonomic classification20182020120[182]
PhyloPhlAnhttp://segatalab.cibio.unitn.it/tools/phylophlan/Taxonomic classification20132020448[183]
BASyshttp://wishart.biology.ualberta.ca/basysGenome annotation2005–333[197]
RASThttps://rast.nmpdr.org/Genome annotation200820157630[198]
IMG/ERhttp://img.jgi.doe.gov/erGenome annotation20072019833[200]
BG7https://github.com/bg7/BG7Genome annotation2012201352[206]
AAMGhttp://www.cbrc.kaust.edu.sa/indigoGenome annotation2013–70[207]
BEACONhttp://www.cbrc.kaust.edu.sa/BEACON/Genome annotation2015–14[205]
PGAPhttps://github.com/ncbi/pgapGenome annotation201320201723[208]
Prokkahttps://github.com/tseemann/prokkaGenome annotation201420204794[210]
DeNoGAPhttps://sourceforge.net/projects/denogap/Genome annotation201620178[214]
GAMOLA2https://drive.google.com/file/d/0B_fIEHIR2oaabVlzcF9NUTlnbjQ/viewGenome annotation2017–13[215]
DFASThttps://github.com/nigyta/dfast_core/Genome annotation20162020184[216]
MicrobeAnnotatorhttps://github.com/cruizperez/MicrobeAnnotatorGenome annotation2020–0[217]
MetaWRAPhttps://github.com/bxlab/metaWRAPAutomated Pipeline20182020114[161]
SqueezeMetahttps://github.com/jtamames/SqueezeMetaAutomated Pipeline2019202017[224]
ToolAccess linkFunctionFirst releaseLast updatedCurrent citationsReference
PhyloSifthttps://github.com/gjospin/PhyloSiftTaxonomic classification2014–438[159]
GTDB-Tkhttps://github.com/ecogenomics/gtdbtkTaxonomic classification20192020129[176]
lastTaxahttps://gitlab.com/jfroula/lasttaxaTaxonomic classification––––
BAT–Taxonomic classification2019–15[168]
MiGAhttp://microbial-genomes.org/Taxonomic classification20182020120[182]
PhyloPhlAnhttp://segatalab.cibio.unitn.it/tools/phylophlan/Taxonomic classification20132020448[183]
BASyshttp://wishart.biology.ualberta.ca/basysGenome annotation2005–333[197]
RASThttps://rast.nmpdr.org/Genome annotation200820157630[198]
IMG/ERhttp://img.jgi.doe.gov/erGenome annotation20072019833[200]
BG7https://github.com/bg7/BG7Genome annotation2012201352[206]
AAMGhttp://www.cbrc.kaust.edu.sa/indigoGenome annotation2013–70[207]
BEACONhttp://www.cbrc.kaust.edu.sa/BEACON/Genome annotation2015–14[205]
PGAPhttps://github.com/ncbi/pgapGenome annotation201320201723[208]
Prokkahttps://github.com/tseemann/prokkaGenome annotation201420204794[210]
DeNoGAPhttps://sourceforge.net/projects/denogap/Genome annotation201620178[214]
GAMOLA2https://drive.google.com/file/d/0B_fIEHIR2oaabVlzcF9NUTlnbjQ/viewGenome annotation2017–13[215]
DFASThttps://github.com/nigyta/dfast_core/Genome annotation20162020184[216]
MicrobeAnnotatorhttps://github.com/cruizperez/MicrobeAnnotatorGenome annotation2020–0[217]
MetaWRAPhttps://github.com/bxlab/metaWRAPAutomated Pipeline20182020114[161]
SqueezeMetahttps://github.com/jtamames/SqueezeMetaAutomated Pipeline2019202017[224]
Table 4
Open in new tab

MAG taxonomic classification and annotation tools

ToolAccess linkFunctionFirst releaseLast updatedCurrent citationsReference
PhyloSifthttps://github.com/gjospin/PhyloSiftTaxonomic classification2014–438[159]
GTDB-Tkhttps://github.com/ecogenomics/gtdbtkTaxonomic classification20192020129[176]
lastTaxahttps://gitlab.com/jfroula/lasttaxaTaxonomic classification––––
BAT–Taxonomic classification2019–15[168]
MiGAhttp://microbial-genomes.org/Taxonomic classification20182020120[182]
PhyloPhlAnhttp://segatalab.cibio.unitn.it/tools/phylophlan/Taxonomic classification20132020448[183]
BASyshttp://wishart.biology.ualberta.ca/basysGenome annotation2005–333[197]
RASThttps://rast.nmpdr.org/Genome annotation200820157630[198]
IMG/ERhttp://img.jgi.doe.gov/erGenome annotation20072019833[200]
BG7https://github.com/bg7/BG7Genome annotation2012201352[206]
AAMGhttp://www.cbrc.kaust.edu.sa/indigoGenome annotation2013–70[207]
BEACONhttp://www.cbrc.kaust.edu.sa/BEACON/Genome annotation2015–14[205]
PGAPhttps://github.com/ncbi/pgapGenome annotation201320201723[208]
Prokkahttps://github.com/tseemann/prokkaGenome annotation201420204794[210]
DeNoGAPhttps://sourceforge.net/projects/denogap/Genome annotation201620178[214]
GAMOLA2https://drive.google.com/file/d/0B_fIEHIR2oaabVlzcF9NUTlnbjQ/viewGenome annotation2017–13[215]
DFASThttps://github.com/nigyta/dfast_core/Genome annotation20162020184[216]
MicrobeAnnotatorhttps://github.com/cruizperez/MicrobeAnnotatorGenome annotation2020–0[217]
MetaWRAPhttps://github.com/bxlab/metaWRAPAutomated Pipeline20182020114[161]
SqueezeMetahttps://github.com/jtamames/SqueezeMetaAutomated Pipeline2019202017[224]
ToolAccess linkFunctionFirst releaseLast updatedCurrent citationsReference
PhyloSifthttps://github.com/gjospin/PhyloSiftTaxonomic classification2014–438[159]
GTDB-Tkhttps://github.com/ecogenomics/gtdbtkTaxonomic classification20192020129[176]
lastTaxahttps://gitlab.com/jfroula/lasttaxaTaxonomic classification––––
BAT–Taxonomic classification2019–15[168]
MiGAhttp://microbial-genomes.org/Taxonomic classification20182020120[182]
PhyloPhlAnhttp://segatalab.cibio.unitn.it/tools/phylophlan/Taxonomic classification20132020448[183]
BASyshttp://wishart.biology.ualberta.ca/basysGenome annotation2005–333[197]
RASThttps://rast.nmpdr.org/Genome annotation200820157630[198]
IMG/ERhttp://img.jgi.doe.gov/erGenome annotation20072019833[200]
BG7https://github.com/bg7/BG7Genome annotation2012201352[206]
AAMGhttp://www.cbrc.kaust.edu.sa/indigoGenome annotation2013–70[207]
BEACONhttp://www.cbrc.kaust.edu.sa/BEACON/Genome annotation2015–14[205]
PGAPhttps://github.com/ncbi/pgapGenome annotation201320201723[208]
Prokkahttps://github.com/tseemann/prokkaGenome annotation201420204794[210]
DeNoGAPhttps://sourceforge.net/projects/denogap/Genome annotation201620178[214]
GAMOLA2https://drive.google.com/file/d/0B_fIEHIR2oaabVlzcF9NUTlnbjQ/viewGenome annotation2017–13[215]
DFASThttps://github.com/nigyta/dfast_core/Genome annotation20162020184[216]
MicrobeAnnotatorhttps://github.com/cruizperez/MicrobeAnnotatorGenome annotation2020–0[217]
MetaWRAPhttps://github.com/bxlab/metaWRAPAutomated Pipeline20182020114[161]
SqueezeMetahttps://github.com/jtamames/SqueezeMetaAutomated Pipeline2019202017[224]
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