Has anyone used MeDuSa: a multi-draft based scaffolder

Question

[Optimist]

Hi All,

Has anyone used Medusa tool to construct scaffolds from contigs? How was the experience been like? Is it 'safe' to construct scaffold in this method as it introduces 'N's in between?

kindly give your inputs on these

Thanks & Regards

Optimist

Answer 1

[h.mon]

MeDuSa has been cited 55, so it seems it is moderately used. To find out how reliable MeDuSa is, you can try to browse the list of citing papers and find an independent review / comparison of scaffolding methods.

Is it 'safe' to construct scaffold in this method as it introduces 'N's in between?

To produce a linear representation of the genome, all scaffolders will insert Ns when joining contigs, as the sequence between these contigs is missing and thus, unknown.