Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets

Table 1 Description of the publicly available mock community datasets used for this experiment

Label	Technology	Mock community	Species	Abundances	Reads used	Median length	Mean length	Total bases (Gb)	Median QV	Release date	Source
HiFi ATCC MSA-1003	PacBio HiFi	ATCC MSA-1003	20^a	Staggered (14–0.02%)	2,419,037	8,310	8,492	20.54	36	6/4/19	NCBI: SRX6095783
HiFi Zymo D6331	PacBio HiFi	ZymoBIOMICS D6331	17^b	Staggered (18–0.0001%)	1,978,852	8,077	9,092	17.99	40	11/25/20	NCBI: SRX9569057
ONT R10 Zymo D6300	Oxford Nanopore Technologies	ZymoBIOMICS D6300	10^c	Even (12%, 2%)	275,318^d	6,664	12,022	3.31	10	2/7/20	https://lomanlab.github.io/mockcommunity/r10.html
ONT Q20 Zymo D6300	Oxford Nanopore Technologies	ZymoBIOMICS D6300	10^c	Even (12%, 2%)	2,000,000^d	4,160	4,805	9.61	N/A	3/23/21	ENA: ERR5396170
Illumina ATCC MSA-1003	Illumina	ATCC MSA-1003	20^a	Staggered (14–0.02%)	10,038,314	125	125	1.25	37	12/2018	NCBI: SRX5169925
Illumina Zymo D6300	Illumina	ZymoBIOMICS D6300	10^c	Even (12%, 2%)	20,000,000^e	150	150	2.99	37	7/2020	NCBI: SRX8824472

^a20 bacteria
^b14 bacteria, 1 archaea, 2 yeasts
^c8 bacteria (at 12% abundance), 2 yeasts (at 2% abundance)
^dLength-filtered to eliminate reads < 2 kb and > 50 kb from starting set of 1.16 million reads (ONT R10) and 5.4 million reads (ONT Q20);
^eSubsampled from ~ 103 million available reads

ISSN: 1471-2105