LotuS: an efficient and user-friendly OTU processing pipeline

Microbiome

Table 2 Computational efficiency

Dataset	Time (s)	Lotus_RDP	Lotus_BLAST	QIIME DN	QIIME Ref	mothur
2 × 454	Demultiplexing/quality filtering	37	37	160	160	235
2 × 454	Full run	177	7,317	4,325	17,081	39,660
2 × MiSeq	Demultiplexing/quality filtering	820	820	3,495	3,495	*
2 × MiSeq	Full run	8,856	23,761	69,696	56,916	*

Execution times for the five pipelines in seconds performed on the same computer. The output of “full runs” is OTU abundance, higher taxonomic level abundance and a phylogenetic tree of OTUs. The table is further separated into the execution times on our 454 mice faeces test set (2 × 454) and the two human faeces MiSeq test sets (2 × MiSeq). Asterisks denote that mothur was excluded, due to an unknown error (see Additional file 1).

ISSN: 2049-2618