BULLET: a computer simulation of shotgun DNA sequencing

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Abstract
BULLET is a computer program that simulates shotgun sequencing of DNA. The program has been used to simulate the sequencing of DNA fragments from 2 to 30kb. To obtain 80% single or double-stranded sequence, a doubling of the DNA fragment size necessitates twice the nwnber of sequencing reactions. However, a similar linear relationship does not apply to the determination of 100% single or double-stranded sequence. Data from BULLET were used to derive simple linear formulae that estimate the number of sequencing reactions necessary to partially sequence a fragment of DNA irrespective of size. When 80% of the double-stranded sequence has been determined, ∽98% of single-stranded sequence will be known. This is a reasonable point to change to a more directed strategy of DNA sequencing.

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