Shotgun sequencing is a type of de novo sequencing, meaning it can assemble an entire genome that has not yet been sequenced before.
Shotgun sequence is used to analyze DNA sequences longer than 1000 base pairs, up to entire chromosomes. The basic methodology is to break up multiple sequences of the same genome in various places, and reassemble them based on overlapping regions.
Statistically speaking, there are chances of false contigs coming up. This occurs when the assembler finds overlapping segments that occurred by chance. This may be corrected by paired-ends or mate-pairs sequencing.
Additionally, transfecting bacteria cells can take a long time.
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