Appendix 1: Glossary
accessory genome
The collection of genes that are not present in all genomes in a given set of genomes (see also
core genome, pan-genome)
alignment
A method of comparing two or more sequences, usually displayed as rows in a matrix or array;
may be either local or global
assembly
A construct formed by joining overlapping sequence reads into contiguous strings of sequence
(contigs) that acts as a representation of the organism genome; may be either partial (draft)
assembly or complete (closed) assembly
bioinformatics
The processes and algorithms involved in managing and analysing sequencing data
BLAST
Basic Local Alignment Search Tool – an algorithm that uses local alignment to match sequences
against a database for identification (see also local alignment)
consensus
The base called by the majority of overlapping sequences or reads at a given locus; can also be
expressed as a percentage eg. 90% consensus = 9 out of every 10 reads called the same base at
that particular locus
contig
A contiguous sequence formed by the consensus sequence from overlapping reads
core genome
The collection of genes that are present in all genomes in a given set of genomes (see also
accessory genome, pan-genome)
coverage
The amount of an entire genome sequence covered by mapped reads; sometimes also used to refer
to “depth of coverage” (see depth)
depth
The number of overlapping reads that map to a given locus eg. 100x depth = 100 reads mapped
to that particular locus
exome
The collective protein-coding regions of a genome
genome
The total genetic content of an organism
genomics
The study and analysis of genomes
global alignment
The process of aligning each locus in two or more sequences of similar length for comparison,
resulting in an alignment of sequences of equal length (see also local alignment)
GUI
Graphical User Interface – an interactive program interface that utilises graphical elements such
as icons and “point-and-click” options in a window to facilitate ease of use
GWAS
Genome-Wide Association Study – a study that attempts to match genetic alleles with a specified
phenotype within a population
haploid
A single chromosome per genome (see also polyploid)
homopolymer
A sequence string of identical bases eg. GGGGGGGG or AAAA
horizontal gene transfer
Any lateral transfer of genetic material including through conjugation, transduction,
transformation, plasmid transfer
indel
Mutation that involves either insertion and/or deletion of bases
insertion sequence
A short sequence of DNA that can move from one position on a chromosome to another; also
known as an IS element
local alignment
The process of aligning each locus in a shorter sequence against a corresponding section of a
longer sequence or database for comparison (see also global alignment, BLAST)
locus
A position in a genome sequence occupied by a single nucleotide
metagenomics
The study and analysis of all the genomic content in a sample (frequently involves multiple
organisms)
models of DNA evolution
Models that aim to predict the rate and direction of nucleotide substitution during evolution eg.
Jukes & Cantor, Generalised Time-Reversible, Hasegawa, Kishino & Yano; usually incorporated
into maximum likelihood and Bayesian models to estimate a phylogeny
molecular clock
The natural background rate of evolutionary change in a genome that is assumed to exist
N50
A genome assembly metric – the N50 is the contig length where the sum of the contigs of that
length or longer comprise ≥50% of the total sum of contig lengths, and the sum of the contig of
that length or shorter comprise ≥50% of the total sum of contig lengths
neighbour-joining
A rapid clustering method to draw a phylogenetic tree; other more probabilistic methods include
maximum likelihood and Bayesian analysis
open source
Software that is publicly available and free
pan-genome
The total collection of genes present in a given set of genomes. Pan-genome = core genome +
accessory genome
Phred-score
A per-base score to indicate the quality and accuracy of sequencing; Q10 = 1 error per 10 bases,
Q20 = 1 error per 100 bases, Q30 = 1 error per 1000 bases
phylogeny
The history of the genetic evolution of a group of organisms; usually represented by a
phylogenetic tree, where branches represent the genetic differences between organisms
polyploid
Multiple chromosomes per genome (see also haploid)
read clipping
A post-sequencing bioinformatics quality-control process where raw sequence reads are filtered
and trimmed to remove indexing adaptors attached to the DNA sequence during library
preparation, and to remove low quality sequence regions
read mapping
The process of aligning/matching sequence reads against corresponding regions of a reference
genome
reads
The raw, usually overlapping, unanalysed sequence output from a genome sequencer, that can be
either mapped to a reference genome, or assembled de novo into contigs; length varies depending
on the sequencer and intended study
recombination
Any process involving the horizontal exchange of genes between two organisms
reference genome
A representative (usually complete / closed) genome
scaffold
A genome framework, comprising several contigs, separated by expected gaps of a known size
SNP
Single nucleotide polymorphism – a single base variation
transcriptome
The sum of all transcribed RNA produced by a set of organisms