Table 4 |
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|
Comparison of results of INDUS with other binning methods for Sargasso sea sample 1* metagenomic data set. |
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|
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 |
||
|
|
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|
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. |
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|
Mohammed et al. BMC Genomics 2011 12(Suppl 3):S4 doi:10.1186/1471-2164-12-S3-S4 |
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