Alpha and beta diversity
Measures for community richness within an environment or variation between different environments
Aligning and merging short fragments of sequenced DNA in order to reconstruct the original genome.
Average number of times a base of a genome is sequenced.
Contiguous fragments of DNA sequence from an incomplete draft genome.
The GC content of a DNA sequence is the percentage of nucleotides that are either G or C.
Giga base pairs (Gb)
Size of a metagenomics sample in numbers of base pairs
Horizontal gene transfer (HGT)
Exchange or absorption of genetic material independent of reproduction
Environmental gene tags (EGTs)
Short DNA sequences that characterize microbial environments.
Collection of biological DNA fragments prepared for sequencing
A microbial ecosystem is the community of all microbes living in a specific environment
Identifying the complete set of transcripts (RNA-seq) from microbial environments
profiling of community-wide protein abundances
Multilocus sequence typing (MLST)
Technique to detect variability of housekeeping genes for identifying bacterial strains
DNA fragments from different samples are pooled and sequenced all together
Operational taxonomic units (OTU)
Sequence based species cluster defined by 16S gene sequence similarity
Functional identical genes in different species that evolved from a common ancestral gene
The entire gene set of a species
Phred score (Q score)
Quality value for each sequenced base
Reads per kilo base per million (RPKM)
Normalization to compare coverage of genes
Ribosomal sequences 16S
To identify and compare bacteria based on differences in their 16S ribosomal sequence
How deep is enough for metagenomic shotgun sequencing
Identifying the gene composition of individual strains in metagenomic samples