3${}^{\prime }$/5${}^{\prime }$ Transcriptomics	Approaches to transcriptomics that synthesise cDNA from the 3${}^{\prime }$ or alternatively the 5${}^{\prime }$ of a transcript. These approaches typically possess greater depth of coverage within 150 bp of the respective ends of the transcript.
Breadth of coverage	The proportion of bases in a target genome that attained a certain depth of coverage threshold. The breadth of coverage is therefore depth threshold dependent.
CellRanger	A software platform offered by 10× genomics to process data output from their broad range of protocols.
De-duplication	Input cDNA from many single cell platforms undergoes PCR amplification to enable the small amount of RNA from individual cells to be read on next-generation sequencing platforms. De-duplication is the process by which reads derived from the same starting cDNA molecule are grouped together, and a representative read is chosen. This quantifies how many molecules were present prior to PCR and counteracts PCR amplification bias.
Depth of coverage	The number of reads from a sequencing experiment that align to a particular base in the genome. This can be in bulk or broken down per cell.
Full-length transcriptomics	Approaches to transcriptomics that obtain sequence data covering the entire length of a transcript. For instance, the Smart-Seq2 platform.
Long-read sequencing	Sequencing on machines capable of obtaining sequences from reads in excess of 1000 Kbp. This includes machines offered by Oxford Nanopore and Pacific Biosciences.
mgatk	Mitochondrial Genome Analysis Toolkit. A computational tool developed to obtain high-quality variants from mtscATAC-seq data for lineage tracing.
mtscATAC-seq	Mitochondrial single-cell assay for transposase-accessible chromatin with sequencing. A high-throughput approach for genotyping mitochondria and obtaining chromatin accessibility in single cells.
Multiplexing	In high-throughput single-cell approaches, reads are barcoded with a nucleotide sequence to identify which cell they come from. This enables reads from many cells to be pooled together on the same flowcell during sequencing, thereby increasing throughput. This pooling is termed multiplexing.
NUMT	Nuclear DNA of mitochondrial origin. These homologous sequences can result in errors of heteroplasmy quantification when using short-read sequences.
PCR stutter	A technical error occurring during PCR, typically near short tandem repeats, resulting in base pairs randomly being skipped during PCR. This results in reads derived from the same transcript having different starting alignment positions.
scATAC-seq	Single-cell Assay for Transposase Accessible Chromatin using sequencing. A single-cell omics approach for obtaining chromatin accessible regions of the genome, an epigenomic cell state.
scRNA-seq	Single-cell RNA sequencing. A single-cell omics approach for obtaining transcriptional state.
Short-read sequencing	Sequencing on machines that are typically capable of sequencing reads approximately 150–300 bp in length. Illumina short-read sequencers are a common platform used for this approach.
TCR	T-cell receptors are proteins used by T-cells for detecting antigens from foreign bodies. Many different TCRs are used by the immune system to detect a broad range of potential pathogens. Roughly ${10}^{15}$ possible TCR sequences exist, of which only ${10}^{11}$ will be found in an individual human, making it unlikely that two identical TCR sequences will emerge independently in the same person. TCR sequences can therefore be used to lineage trace T-Cells as any two cells sharing this sequence will likely be derived from a common ancestor.
Variant	Positions where sequenced reads differ from a reference genome. This is used to infer the presence of mutations.
V(D)J Recombination	The process by which different TCR sequences are produced during thymic maturation.