Table 1.
Summary of sequencing methods for microbiome profiling
|
Method |
Sequencing type |
Sequencing platform |
Read lengths (bp) |
No. of reads per sample (M) |
Output |
Data processing required |
Cost per sample |
|---|---|---|---|---|---|---|---|
|
SRA (V3-V4) |
Amplicon |
Illumina MiSeq |
250 or 300 |
0.03–0.2 |
Taxonomic profiling (genus level) |
Low |
$ |
|
LRA (16S-ITS-23S) |
Amplicon |
PacBio Sequel II |
~2500 |
0.01–0.03 |
Taxonomic profiling (strain or species level) |
Low |
$ |
|
SRM (short-read metagenomics) |
Metagenome |
Illumina NovaSeq 6000 |
150 |
20–100 |
Taxonomic and functional profiling, genome assembly and binning |
High |
$$ |
|
LRM (long-read metagenomics) |
Metagenome |
PacBio Sequel II |
7000 to>10 000 |
1.5–3 |
Taxonomic and functional profiling, genome assembly and binning |
Moderate |
$$$ |