I am using SPAdes to assemble ten samples all of the same genome, Arabidopsis ecotype ws-0. Nine of the samples have an ~ 2 kb insert. However, if the samples are tetraploid and the insert is in only present in 1 set of chromosomes (in just one place, not two allelles), then the coverage for the insert would be expected to be one-eighth that of the rest of the genome, so will SPAdes include the insert in its assembly or leave it out because of the relatively low coverage of the insert to the rest of the genome ?
I am using SPAdes to assemble ten samples all of the same genome, Arabidopsis ecotype ws-0. Nine of the samples have an ~ 2 kb insert. However, if the samples are tetraploid and the insert is in only present in 1 set of chromosomes (in just one place, not two allelles), then the coverage for the insert would be expected to be one-eighth that of the rest of the genome, so will SPAdes include the insert in its assembly or leave it out because of the relatively low coverage of the insert to the rest of the genome ?