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] |