From: Strain-level epidemiology of microbial communities and the human microbiome
Method | Platform | Authors’ description | Reference |
---|---|---|---|
Oligotyping | 16S rRNA gene amplicon | “oligotyping... Focus [es] on the variable sites revealed by the entropy analysis to identify highly refined taxonomic units” | [112] |
Sub-OTU clustering | 16S rRNA gene amplicon | “we combine error-model-based denoising and systematic cross-sample comparisons to resolve the fine (sub-OTU) structure of moderate-to-high-abundance community members” | [113] |
MED | 16S rRNA gene amplicon | “MED uses information uncertainty among sequence reads to iteratively decompose a dataset until the maximum entropy criterion is satisfied for each final unit” | [114] |
DADA2 | 16S rRNA gene amplicon | “DADA2 implements a new quality-aware model of Illumina amplicon errors. Sample composition is inferred by dividing amplicon reads into partitions consistent with the error model.” | [115] |
Deblur | 16S rRNA gene amplicon | “Deblur … compares sequence-to-sequence Hamming distances within a sample to an upper-bound error profile combined with a greedy algorithm to obtain single-nucleotide resolution.” | [116] |
UNOISE2 | 16S rRNA gene amplicon | “UNOISE2... Cluster [s] the unique sequences in the reads. A cluster has a centroid sequence with higher abundance plus similar sequences having lower abundances.” | [117] |
PathoScope | Shotgun metagenomic | “PathoID … reassign [s] ambiguously aligned sequencing reads and accurately estimate [s] read proportions from each genome in the sample.” | [118] |
LSA | Shotgun metagenomic | “LSA... separates reads into biologically informed partitions and thereby enables assembly of individual genomes.” | [119] |
PanPhlAn | Shotgun metagenomic | “PanPhlAn identifies which genes are present or absent within different strains of a species, based on the entire gene set of the species’ pangenome.” | [66] |
MetaMLST | Shotgun metagenomic | “MetaMLST performs an in silico consensus sequence reconstruction of the allelic profile of the microbial strains in a metagenomics sample.” | [120] |
MIDAS | Shotgun metagenomic | “MIDAS … is a computational pipeline that quantifies bacterial species abundance and intra-species genomic variation from shotgun metagenomes.” | [37] |
ConStrains | Shotgun metagenomic | “ConStrains … exploits the polymorphism patterns in a set of universal bacterial and archaeal genes to infer strain-level structures in species populations.” | [121] |
StrainPhlAn | Shotgun metagenomic | “StrainPhlAn … is based on reconstructing consensus sequence variants within species-specific marker genes and using them to estimate strain-level phylogenies.” | [8] |
metaSNV | Shotgun metagenomic | “metaSNV … performs SNV calling for individual samples and across the whole data set, and generates various statistics for individual species” | [102] |
DESMAN | Shotgun metagenomic | “DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles.” | [122] |