MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities

Table 1 Sequence read processing efficiency of MetaPro, HUMAnN3, and SAMSA2

Dataset	Pipeline	Mean % of total reads that are putative mRNA	Mean % of annotated putative reads	Mean annotated putative reads, as a % of total reads	Mean unique gene families^a
NOD mouse	MetaPro	17.16	71.64	12.73	14,308
NOD mouse	HUMAnN3	79.95	2.80	2.24	2691
NOD mouse	SAMSA2	39.33	10.85	4.27	11,499
Kimchi	MetaPro	32.21	59.27	19.09	87,193
Kimchi	HUMAnN3	89.26	11.71	10.45	9166
Kimchi	SAMSA2	72.54	15.72	11.4	86,270
Oral Biofilm	MetaPro	97.48	96.96	94.52	95,707
Oral Biofilm	HUMAnN3	100	71.31	71.31	28,750
Oral Biofilm	SAMSA2	98.98	80.40	79.58	298,315

^aUnlike MetaPro and SAMSA2, HUMAnN3 reports only the number of unique gene families

ISSN: 2049-2618