Table 1 Tools for metagenomic strain analysis

Oligotyping

16S

–

–

–

–

[42]

Long-read 16S

16S

–

–

–

–

[119]

Minimum entropy decomposition

16S

–

–

–

–

[39]

OTU subpopulations

16S

–

–

–

–

[40]

LEA-seq

16S

–

–

–

–

[41]

DADA2

16S

No

Poisson modeling of sequence errors (the Divisive Amplicon Denoising Algorithm)

Yes

–

[43]

UNOISE2

16S

No

Abundance-based identification of sequencing errors

Yes

–

[44]

Deblur

16S

No

Abundance-based identification of sequencing errors

Yes

–

[45]

Megan

WGS

Yes

Lowest common ancestor algorithm

No

Not reported

[120]

GSMer

WGS

Yes

Unique strain-level markers (k-mers)

No

0.25×

[121]

WG-FAST

WGS

Yes

SNVs

No

3×

[122]

StrainPhlAn

WGS

Yes

SNVs within species-level marker genes

Yes

10×

[6]

PanPhlAn

WGS

Yes

Unique combinations of species-level marker genes

Yes

1×

[6]

MIDAS

WGS

Yes

Unique strain-level marker genes

Yes

Not reported

[37]

Sigma

WGS

Yes

Likelihood-based

No

0.027×

[123]

PathoScope

WGS

Yes

Likelihood-based

No

Less than 1×

[124]

ConStrains

WGS

Yes

Inferred haplotype-like SNP profiles

Yes

10×

[4]

LSA

WGS

De novo assembly

SVD-based K-mer clustering

Yes (not validated)

25 ~ 50×

[125]

CNV-based methods

WGS

Yes

[126]