Hi Members
I am using Assembly tools to generate contigs and scaffolds. One tool gives contigs with higher N50 than another tool. The same tool however gives scaffolds with lower N50 than the other tool. Should I use contigs or the scaffolds to conduct analysis such as comparing with the reference genome ? Scaffolds are essentially set of contigs with estimates of gaps in between which are represented by Ns.
Aby
I am using Assembly tools to generate contigs and scaffolds. One tool gives contigs with higher N50 than another tool. The same tool however gives scaffolds with lower N50 than the other tool. Should I use contigs or the scaffolds to conduct analysis such as comparing with the reference genome ? Scaffolds are essentially set of contigs with estimates of gaps in between which are represented by Ns.
Aby
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