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Table 1 Tools for metagenomic strain analysis

From: Experimental design and quantitative analysis of microbial community multiomics

Tool Data type Requires reference genome? Method to resolve ambiguous reads New strain detection Recommended minimal coverage Reference
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 [122]
StrainPhlAn WGS Yes SNVs within species-level marker genes Yes 10× [6]
PanPhlAn WGS Yes Unique combinations of species-level marker genes Yes [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 Target gene or region copy number variation [126]
  1. CNV copy number variation, LEA-Seq low-error amplicon sequencing, OTU operational taxonomic unit, SNP single nucleotide polymorphism, SNV single-nucleotide variant, SVD singular-value decomposition, WGS whole-genome sequencing