Introduction to metagenomics

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What are the limitations related to microbial analysis with marker genes (e.g. 16S rRNA)?

They need a high number of sequences in comparison to shotgun metagenomics

Definition of OTUs is arbitrary and sometimes don't match with "real species"

It is difficult to identify microbes at species and strain level

They have a lower taxonomic resolution in comparison to shotgun metagenomics

Chimeras can be present in the molecules undergoing sequencing

What do they have in common these resources: RDP, rrnDB, Silva, GreenGenes

All are databases including shotgun metagenomics sequences

All are databases for analysing 16S rRNA sequences

All are databases where16S rRNA sequences are deposited

They are bioinformatics tools for analysis of marker gene sequences

What is the common characteristic of PATRIC, GOLD, NCBI microbial genomes resources?

All are databases including microbial genomes

All these include software for analysis of microbial genomes.

All of them are databases for microbial genome sequence analysis

All of them are databases including marker gene sequences.

What is the common characterist of EBI metagenomics, MG-RAST and HMP DACC?

All are databases including shotgun metagenomic sequences.

All include software for analysis metagenomic dataset.

All of them are repositories for microbial genomes.

All are online resources for 16S rRNA analysis.

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