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Table 2 List of metagenomics sequence classification methods and their characteristics sorted by class of method

From: Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities

Method name

Class of method

Sequence alignment method/Composition method

Standalonea/Web server

Most recent year published (first time published)b

Functional classification if applicable

References

Number of citationsc

MEGAN4

Similarity

MEGABLAST, BLASTN, BLASTX, RAPSEARCH2 [32] / N/A

Yes/No

2011 (2007)

KEGG, SEED

[15, 29, 45–47]

1089

MG-RAST

Similarity

BLASTN, BLAT / N/A

No/Yes

2008

SEED, NOG, COG, KEGG

[48]

691

CAMERA

Similarity

All 6 BLAST programs / N/A

No/Yes

2007 (2011)

Pfam, TIGRFAM, COG, KOG, PRK

[49, 50]

324

CARMA3

Similarity

BLASTX, HMMER3 [51] / N/A

Yes/Yes

2011 (2008)

GO

[41, 52, 53]

201

WebMGA

Similarity

FR-HIT [54] / N/A

No/Yes

2013

Pfam, TIGRFAM, COG, KOG, PRK, GO

[55]

54

DiScRIBinATE (SOrt-ITEMS)d

Similarity

BLASTX, RAPSEARCH2 / N/A

Yes/No

2010 (2009)

N/A

[31, 56]

48

Ray Meta

Similarity

Exact match k-mers / N/A

Yes/No

2012

N/A

[57]

34

Kraken

Similarity

Exact match k-mers / N/A

Yes/No

2014

N/A

[28]

15

RTM

Similarity

k-mers / N/A

Yes/Yes

2012

KEGG

[58]

12

Genometa

Similarity

Bowtie [59], BWA [60] / N/A

Yes/No

2012

N/A

[61]

7

LMAT

Similarity

Exact match k-mers / N/A

Yes/No

2013

N/A

[62]

6

Sequedex

Similarity

Exact match k-mers / N/A

Yes/No

2012

N/A

[63]

5

MetaBin

Similarity

BLASTX, BLAT / N/A

Yes/Yes

2012

COG

[64]

4

TAMER

Similarity

MEGABLAST / N/A

Yes/No

2012

N/A

[65]

4

metaBEETL

Similarity

Direct comparison of compressed text indices / N/A

Yes/No

2013

N/A

[7]

2

SPANNER

Similarity

BLASTP / N/A

Yes/No

2013

N/A

[66]

2

GOTTCHA

Similarity

BWA / N/A

Yes/No

2015

N/A

[67]

0

CLARK

Similarity

k-mers / N/A

Yes/No

2015

N/A

[68]

0

MLTreeMap

Marker

BLASTX / N/A

Yes/Yes

2010 (2007)

4 Enzyme families

[69, 70]

206

AMPHORA2

Marker

HMMER3 / N/A

Yes/Yes

2012 (2008)

N/A

[13, 71, 72]

190

MetaPhlAn

Marker

MEGABLAST, Bowtie2 [73] / N/A

Yes/Yes

2012

N/A

[11]

114

MetaPhyler

Marker

BLASTN, BLASTX / N/A

Yes/No

2011

N/A

[30]

42

mOTU

Marker

HMMER3 / N/A

Yes/Yes

2013

N/A

[19]

24

Phylosift

Marker

LAST, HMMER3 / N/A

Yes/No

2014

N/A

[14]

18

phymmBL

Hybrid

MEGABLAST / IMM

Yes/No

2011 (2009)

N/A

[6, 74]

182

RITA

Hybrid

Pipeline of BLAST variations / NB

Yes/Yes

2012 (2011)

N/A

[75, 76]

38

SPHINX

Hybrid

BLASTX / k-means

No/Yes

2010

N/A

[10]

17

TaxyPro

Hybrid

CoMet web server / Mixture model

Yes/No

2013

Pfam

[77]

3

TWARIT

Hybrid

BWA short read alignment [60] / k-means

No/Yes

2012

N/A

[78]

2

PhyloPythiaS

Composition

N/A / SVM

Yes/Yes

2011 (2007)

N/A

[30, 79, 80]

269

TACOA

Composition

N/A / k-NN

Yes/No

2009

N/A

[33]

65

NBC

Composition

N/A / NB

Yes/Yes

2011 (2008)

N/A

[81, 82]

35

RAIphy

Composition

N/A / RAI

Yes/No

2011

N/A

[83]

18

ClaMS

Composition

N/A / DBC signature

Yes/No

2011

N/A

[84]

10

INDUS

Composition

N/A / k-means

No/Yes

2011

N/A

[85]

8

TAC-ELM

Composition

N/A / Neural Network

Yes/No

2012

N/A

[86]

5

MetaCV

Composition

N/A / CV

Yes/No

2013

KEGG

[87]

4

GSTaxClassifier

Composition

N/A / Bayesian

No/No

2010

N/A

[88]

2

  1. N/A not applicable, IMM interpolated Markov model, NB naive Bayes, SVM support vector machine, k-NN k-Nearest Neighbour, RAI relative abundance index, DBC signature de Bruijn chain signature, CV composition vector
  2. aStandalone refers to whether the program can be run locally
  3. bSome methods have had several publications, with later publications regarding improvements on functionality. In these cases the most recent publication was listed, with the first time the method was published in brackets
  4. cNumber of citations is based on Web of Science as of April 21, 2015
  5. dDiScRIBinATE is the successor for SOrt-ITEMS so they were included in the same row