How can I make a reference genome from multiple genomes?

Question

[gamzeozbay]

Hi everyone,

I have low coverage genomes for a species. This species do not have a reference genome that's why we use a different species to map the genome. Is it possible to build a reference genome from these low-coverage genomes? If it is possible, how many genomes do I need?

Sincerely,

Gamze

[Bengisu]

I was wondering the same thing

[samuel.a.odonnell]

If I understand well the idea is to combine the information from the low-coverage samples/strains/isolates/etc to generate an assembly?

Not sure if there is a generic pipeline for this but could you not just try combining all the reads you have and assemble them all together? Which alleles are assembled as the consensus will probably depend on the coverage of each sample and the allele frequency within your samples. You could then map all your samples back onto the assembly to see if they are all represented equally.

[Ankit]

You need to perform de novo assembly using those bits of genome and get a large assembly.