Are alignment results based on a poor-quality genome assembly reliable?

[Liuyj-l]

Dear developer,

I performed whole-genome sequence alignment for 19 species. However, one species has a genome assembly with a BUSCO completeness of only 64%, and two other species have BUSCO completeness of about 89%. Under these circumstances, are the Cactus alignment results reliable? Can they be used for sliding-window phylogenetic analyses, ASTRAL species tree inference, and downstream analyses such as QuIBL?

[glennhickey]

Incomplete genomes will degrade the alignment quality, but outgroups are used to mitigate this. Your best bet is looking at the coverage using halCoverage or taffy coverage.