Wednesday, September 21, 2016

Genomes vs. GenNNNes: The Difference between Contigs and Scaffolds in Genome Assemblies

In recent interactions with the scientific community, we’ve seen a growing number of questions around scaffolding genome assemblies. We thought it might be useful to review the concepts behind contigs and scaffolds, as well as the circumstances in which one might want to scaffold a high-quality PacBio genome assembly. Contigs vs. Scaffolds Contigs are continuous stretches of sequence containing only A, C, G, or T bases without gaps. SMRT Sequencing has all of the necessary performance characteristics – long reads, lack of sequence-context bias, and high consensus accuracy – to generate contiguous genome assemblies with megabase-sized contigs. Ultra-long contigs provide…

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