EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

Table 1 Comparison of EMIRGE with de novo assembly

Method	Community	Number of expected SSUs	Number of SSU sequences or fragments	Number classified at genus level^a	N50	Weighted UniFrac distance
EMIRGE	Simulated simple	10	11	10 (90%)	1,537	0.03
Assembly fragments	Simulated simple	10	78	39 (50%)	383	0.32
EMIRGE	Simulated complex	52^b	23	20 (87%)	1,488	0.04
Assembly fragments	Simulated complex	52^b	320	212 (66%)	122	0.26
EMIRGE	Natural	Unknown	11	9 (82%)	1,484	NA
Assembly fragments	Natural	Unknown	137	85 (62%)	182	0.32^c

^aRDP classifier with bootstrap cutoff > 50%; eukaryotes not classified. ^bWith abundance > 0.5%. ^cDistance to EMIRGE-defined community. NA, Not Applicable: true community structure is unknown

ISSN: 1474-760X