Adapter: Short oligonucleotides which are attached to the DNA to be sequenced. An adapter can provide a priming site for both amplification and sequencing of the adjoining, unknown nucleic acid.

 

Alignment: The mapping of a raw sequence read to a location within a reference genome. The mapping occurs because the sequences within the raw read match or align to sequences within the reference genome.

 

Assembly: Assembly of fragment sequences into higher order structures based on their overlap and reference sequence, where appropriate.

 

BAM: Binary version of SAM file. It is a compressed format for storing SAM data, a typical output of the secondary phase of data analysis. 

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BED: Text file used for genomic intervals, e.g. genes, peak regions etc.

 

Coverage: This value indicates the coverage of an analysed sequence with respect to its length, usually expressed as a percentage; sometimes the term is also used for the depth of reading.

 

Coverage- depth: The number of nucleotides from reads that are mapped to a given position of reference genome.

 

De novo genome assembly: Sequencing of genetic material with no reference sequence available.

 

FASTA: Simple text format for storing raw sequence data. 

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FASTQ: Text format for storing raw sequence data with quality scores for each base. 

 

Paired-end sequencing: Sequencing process where both ends of a single DNA or RNA fragment are sequenced, but the intermediate region is not. Particularly useful for identifying structural rearrangements, including gene fusions.

 

Read: Data output from the analysis of a single fragment (sequence).

 

Read-accuracy: Indicates the occurrence of errors (in %) after primary analysis.

 

Read-depth: The number of sequence reads that pile up at the same genomic location. For example, 30X read-depth coverage indicates that the genomic location is covered by 30 independent sequencing reads. Increased read-depth translates into higher confidence for calling genomic variants.

 

Read-length: The number of base pairs that are sequenced in an individual sequence read.

 

SAM: Text file format for storing sequence alignments against a reference genome. See also BAM.

 

SNP Calling: Process of detecting Single Nucleotide Polymorphisms in the sequences obtained.

 

Variant Calling: Process of detection of sequence variants in the sequences obtained.

 

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