Supercontig

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A supercontig, also known as a super or a scaffold, is the largest type of object in an assembly. A supercontig consists of one or more contigs bound together, all forward-oriented, separated by imprecise gaps (expected size and standard deviation). The supercontig object includes information about the reads and contigs used to generate it, as well as quality scores for each base. The process of creating supercontigs from contigs is called scaffolding.

There are two measures of supercontig length. The true length or gapped length includes gap sizes (both positive and negative), while the reduced length or ungapped length is purely a sum of the lengths of a supercontig's constituent contigs. The airiness of a supercontig is defined as A = 1 - (ungapped length / gapped length).

In Arachne, supercontigs are handled via superb files and the superb object, which defines contig lengths and gap sizes but does not specify bases or quality scores. Note that the "b" in superb means binary, just as in fastb or qualb; it has nothing to do with the English word "superb."

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