Assembly out of mapping reads to a reference genome

Question

[Ric]

Hi, It seems nobody get assembly out of mapping reads to reference genome. Is there a reason why this approach is not good?

Thank you in advance.

Mic

[Rohit]

When mapping reads to a reference genome, what you would have is a consensus, not an assembly. This would be a reference with variants introduced from your mapping data. If you mean to say that assembly of the reads which map to a genome is fragmented, it is due to the uneven coverage, genome complexity and repeats. There are approaches to make local assemblies out of mapped reads, which work to an extent.

[Ric]

Could please provide examples how to make local assemblies out of mapped reads?

[GenoMax]

You can try ABRA for local assemblies.

[Persistent LABS]

You can do both reference-guided as well as denovo genome assembly.

[Ric]

Could you please provide examples for reference-guided assembly?

[GenoMax]

You had started a thread about this 3 months back: Reference guided assembly methods
There is a list of software at Omicstools that you can refer to.