Reads. A collection of clones that over-sample the target genome.

Pair-end reads. Sequence reads derived from both ends of a sequencing-library clone.

Mate-pair reads. Sequence reads derived from both ends of a mate-pair library clone which insert size is usually >1kb.

Insert size. The size of the clone-insert from which a clone-end pair is taken.

Contig. The result of joining an overlapping collection of sequence reads.

Scaffold. The result of connecting non-overlapping contigs by using pair-end reads.

N50 size. As applied to contigs or scaffolds, that size above which 50% of the assembled sequence can be found.

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