An extremely simplified example with only two sequences is as follows:
Original strand : XXXAGCATGCTGCAGTCATGCTTAGGCTAXXXX
First shotgun sequence : XXXAGCATGCTGCAG TCATGCTTAGGCTAXXXX
Second shotgun sequence : TTAGGCTAXXXX XXXAGCATGCTGCAGTCATGC
Reconstructed strand : XXXAGCATGCTGCAGTCATGCTTAGGCTAXXXX
In real-world applications, there are thousands or millions of sequences to deal with, with the addition of transcription and sequencing errors. The computational power required to re-align the sequence in real projects is enormous. For the shotgun sequencing of the human genome in the Human Genome Project run by Celera Genomics in 2000, several supercomputers were running some month nonstop to align all human DNA correctly.
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