How To Obtain A Consensus Sequence From A Genome Assembly File?

Question

[Shivani]

I have a genome assembly file. How do I use it to obtain a consensus sequence for the whole genome.

Is there a tool for this?

Answer 1

[Mensur Dlakic]

There is no consensus sequence, and all the contigs are part of the whole genome. In most cases it is difficult to obtain a single, complete genomic sequence. Instead, we get a certain number of fragments. For high quality assemblies the number of contigs will be low, but assemblies are still useful even with hundreds of contigs.

[Shivani]

OK. Thanks for your answer. I read a paper where they constructed tree from whole genome sequence. https://www.pnas.org/content/114/35/9391

Unable to understand how they got the whole genome sequence. Did they concatenate the individual sequences to get it?