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During a genome assembly, "contiguous sequences of nucleotide bases" (contigs) are built from the multi-alignment of highly similar single reads.
After the alignment step, multiple consensus sequences of all aligned or assembled reads are obtained which represent the contig sequences of a given genome or assembly. In contrast, a scaffold is an ordered set of contigs which are linked by sequences that were derived from the paired-end information of long paired-end libraries (Roche) or mate-pair libraries (Illumina).
Scaffolds always consist of contigs separated by gaps. These gaps might be identified by "NNNN" in a consensus sequence
Ref: http://www.eurofinsdna.com
B. Wajid
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