Contig

In 1980, Staden [4] wrote: In order to make it easier to talk about our data gained by the shotgun method of sequencing we have invented the word "contig".

[5] The bottom-up DNA sequencing strategy involves shearing genomic DNA into many small fragments ("bottom"), sequencing these fragments, reassembling them back into contigs and eventually the entire genome ("up").

Here, a contig still refers to any contiguous stretch of sequence data created by read overlap.

If one end read has a repetitive sequence, as long as its mate pair is located within a contig, its placement is known.

[2] Contig can also refer to the overlapping clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used.

Sets of overlapping clones that form a contiguous stretch of DNA are called contigs; the minimum number of clones that form a contig that covers the entire chromosome comprise the tiling path that is used for sequencing.

Once a tiling path has been selected, its component BACs are sheared into smaller fragments and sequenced.

[2] In this strategy, clones are treated with one or two restriction enzymes and the resulting fragments separated by gel electrophoresis.

These gaps occur if the Bacterial Artificial Chromosome (BAC) library screened has low complexity, meaning it does not contain a high number of STS or restriction sites, or if certain regions were less stable in cloning hosts and thus underrepresented in the library.