Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

Microbiome

Table 2 Median numbers of inferred OTUs from the high complexity mock simulation

Program	cd-hit			usearch			oclust (MSA)			oclust (PW)
Tech./seq. similarity^a (%)	1	2	3	1	2	3	1	2	3	1	2	3
MiSeq 2 × 150	2919	653	351	1758	477	327	2411	979	466	4287	1113	463
MiSeq 2 × 250	8085	2954	676	8413	3148	703	6544	2550	1041	8561	4011	1234
PacBio CCS 450	8555	4686	2449	8479	4870	2390	2053	940	546	1144	427	335
PacBio CCS 750	7910	1991	649	9356	5499	2319	2888	1152	594	757	399	349
PacBio CCS 1450	8488	1231	423	9874	6488	2327	2436	699	370	529	372	322

^aThe simulated technology (vertical); the similarity threshold used for clustering sequences into OTUs (horizontal)

ISSN: 2049-2618