INDUS - a composition-based approach for rapid and accurate taxonomic classification of metagenomic sequences

BMC Genomics

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.

ISSN: 1471-2164