A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome

Table 4 Comparative summary of sequencing depth, reads length, and quality between GS FLEX, PGM, and MiSeq platforms

Platform	Raw reads	Filtered reads^a	Mean Length after filtering (bp)	Percentage of reads kept after filtering	Mean quality score before quality filtering	Number of identified OTUs
Roche 454	118,018	113,306	377	96%	37.7	1028
Ion Torrent PGM	481,593	71,652	297	14.9%	23.4	2747
Illumina Miseq	4,149,441	3,811,042	334	91.8%	37.5	3731

^aNumber of reads after filtering, reads of less than 200 nucleotides and with quality scores below 25 were removed

ISSN: 1471-2180