Interspecific read alignment - Eukaryote

Question

[maxime.policarpo]

Hi everyone,

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,

Maxime