Table 4

Comparison of results of INDUS with other binning methods for Sargasso sea sample 1* metagenomic data set.

Binning method

Total number of sequences

Time taken for analysis (minutes)

Total number of sequences assigned

Cumulative number of sequences assigned at different taxonomic levels


Phylum

Class

Order


INDUS

10000

13

8167

5793

4416

3748

TACOA

10000

180

8870

3518

2739

2545

SOrt-ITEMS

10000

347

8528

8173

6921

5506

MEGAN

10000

321

8866

8417

7559

7461

SPHINX

10000

23

9116

5346

3702

2726



Taxonomic level

Taxon name

Percentage** of sequences assigned


INDUS

TACOA

SOrt-ITEMS

MEGAN

SPHINX


Order

Burkholderiales

22.79

16.75

25.6

28.63

20.31

Alteromonadales

12.81

5.57

17.24

18.65

5.57

Rickettsiales

-

-

5.58

12.78

-

Prochlorales

1.88

-

3.01

2.94

-

Enterobacteriales

-

1.75

-

-

-

Class

Betaproteobacteria

24.31

16.76

28.2

28.89

20.31

Gammaproteobacteria

19.85

9.48

22.91

24.6

16.71

Alphaproteobacteria

-

-

15.55

18.41

-

Flavobacteria

-

-

-

2.12

-

Phylum

Proteobacteria

52.54

32.1

73.6

75.71

47.78

Cyanobacteria

3.73

0.53

4.84

4.83

-

Firmicutes

1.66

1.25

0.27

0.25

4.17

Bacteroidetes

-

0.01

1.97

2.19

-

Tenericutes

-

0.47

-

-

1.51


The cumulative percentage of sequences assigned by INDUS, TACOA, SOrt-ITEMS, MEGAN and SPHINX at order, class and phylum levels

* Sample 1 refers to the subset of 10000 reads from the Sargasso sea data set [18] earlier analysed using MEGAN [2] and SOrt-ITEMS [4]

** Percentages shown are with respect to the total number of sequences (i.e 10000) in the Sample 1 data set. Only those taxa are shown for which at least one of the methods assigned a minimum of 1.5% of the sequences in the data set.

Mohammed et al. BMC Genomics 2011 12(Suppl 3):S4   doi:10.1186/1471-2164-12-S3-S4

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