Adaptor / Adapter: Short single- or double-stranded oligonucleotides that can be ligated to DNA or RNA fragments to barcode or amplify those fragments
Amplicon Sequence Variant (ASV): A unique sequence read, that is the result of a pipeline that corrects for quality and errors (i.e., denoises), which can be used as a proxy for a unique species
Contig: A continuous DNA sequence assembled from a series of short, overlapping sequences
De Novo Assembly: Constructing a novel genome assembly resulting in a reference genome; assembling a genome of a species without prior data of that species’ genome to align or compare to
DNA Sequence: The sequential order of nucleotides composing DNA
Genome: Complete genetic information of an organism
Genome Assembly: A computational representation of a genome sequence built by aligning and merging DNA sequence fragments in order to mimic the original sequence
Indel: Insertion or deletion of a specific nucleotide sequence within a genome
K-mer: All the possible nucleotide sequences of a certain length, ex. K=2 all the possible kmers are: AA AT AC AG TA TT TC TG CA CT CC CG GA GT GC GG
Next Generation Sequencing (NGS): DNA sequencing technologies that produce millions or billions of short reads (25-500bp) quickly and efficiently.
Nx: The largest contig size at which at least x% of bases are contained in contigs of least this length ex. if N50 = 60 - at least half of the nucleotides in the assembly belongs to contigs with the N50 length of 60 nucleotides or longer
Operational Taxonomic Unit (OTU): A taxonomic unit, derived from sequence clustering approaches. Traditionally, this has included data without denoising.
Ortholog: A homologous gene found in different species that can be traced back to a common ancestral genome
Read: The DNA sequence of one fragment, or section of DNA
Read depth: The number of separate reads from Next Generation Sequencing for a specific genomic region
Read group: A set of NGS reads that were all the product of a single sequencing run on one lane
Reference Genome: A fully sequenced, assembled, and preferably annotated genome of an individual representative of a specific species, where other genomic data can then be aligned and interpreted against the original or “reference”; the product of de novo assembly
Repetitive element: A sequence of nucleotides in DNA that occur in multiple copies across the genome
Resequence: Sequencing the genome of an individual of a certain species where a reference genome exists; sequences are aligned to the reference genome for assembly
Scaffold: A portion of a genome sequence assembled from contigs, often containing gaps between those contigs
Third Generation / Long-read Sequencing: DNA sequencing technologies that produce sequence reads measuring thousands of base pairs or longer
References:
Allendorf, F. W., Funk, W. C., Aitken, S. N., Byrne, M., Luikart, G., & Antunes, A. (2022). Conservation and the Genomics of Populations (3rd ed.). Oxford University Press. https://doi.org/10.1093/oso/9780198856566.001.0001.