I have the genomic sequences of a non-model organism that is a fish species. However, the read coverage is too low to make a good genome assembly, and I would have liked to align these reads to a good reference genome. However, the datation of the most recent common ancestor of this species with the closest sequenced species in public databases is 100Mya ago.
I was wondering if someone knew any good aligner that could perform interspecific alignment and if it is worth to try with that much distance between two species ?
Thanks for your help and advices,