Find chromosomal location of a scaffold

Question

[Jautis]

For two closely related species, is there an easy way to align genome assemblies?

Species A is a chromosomal assembly (although it has gaps) and Species B is assembled into smaller scaffolds. I would like to figure out where Species B scaffolds lie on the Species A assembly in order to leverage annotations that are available for A but not B.

Thank you very much!

Answer 1

[h.mon]

See this answer. You can also use bwa mem, minimap2, Blat, among others.

For annotation transfer, see RATT.

[Jautis]

Thanks for the response. However, the answer and methods you refer me to have to do with mapping reads to a genome. What I'm interested in doing is aligning fasta genomes to each other (or rather, finding the chromosome location scaffold X corresponds with).

[h.mon]

The question indeed is about mapping reads to a second reference genome, but no, the answer I linked is not about mapping reads to a genome, it is about aligning scaffolds to a complete genome:

Don't map the reads back to the Zebra Finch genome.

MUMmer is one of the programs commonly used for aligning contigs / scaffolds to reference genomes, and is a requirement for RATT, which is a software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

edit: just to clarify, bwa mem, minimap2 and Blast are all also used for contig / scaffold mapping to a reference genome, with the requirement the reference genome should be close and reasonably similar to the query contig / scaffolds - I believe at most 10-15% difference, someone will correct me if I got the numbers wrong.

[Jautis]

Thanks for the clarification!

[h.mon]

I had indeed provided the wrong link, I linked to a comment to the answer I wanted to link. I've corrected it now.