How does of 16S/18S/ITS Amplicon Metagenomic Sequencing work?
Amplicon metagenomic sequencing is an effective way to investigate all microorganisms present in diverse samples, including:
Targeting and identifying the organisms of interest Annotating and classifying plentiful microorganisms in one assay, to obtain a complete composition of microbial communities Distinction of bacteria and archaea (16S), or fungi and other eukaryotes (ITS/18S) Analyzing samples from physiological fluids or tissues to diagnose disease and cancers
Workflow of Amplicon Metagenomic Sequencing
nfcore/ampliseq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.
Pipeline summary
By default, the pipeline currently performs the following:
Sequencing quality control (FastQC) Trimming of reads (Cutadapt)
Infer Amplicon Sequence Variants (ASVs) (DADA2)
Excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof (QIIME2)
PICRUSt2 - Predict the functional potential of a bacterial community
Calls differentially abundant taxa (ANCOM)
Creates phyloseq R objects (Phyloseq)
Alpha diversity plot
Alpha diversity refers to the diversity of species within a particular area or ecosystem, expressed by the number of species (species richness) present there. There are many metrics to measure alpha diversity, includingObserved,Chao1,ACE,Shannon,Simpson,InvSimpson,Fisher. Google “alpha diversity metrics” for more info.
Significantly differentiated families
The families and phyla of above mentioned taxa are plotted below for an overview. Other ranks can also be plotted if needed.
