Build canine dna.primary_assembly.fa for kb ref

Question

[Candice]

I am following the instruction to build the index using kb.

The command should be

kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 /
intron_t2c.txt --workflow lamanno -n 8 /
Mus_musculus.GRCm38.dna.primary_assembly.fa.gz /
Mus_musculus.GRCm38.98.gtf.gz

In Ensembl dog genome, there is no such file as dna.primary_assembly.fa.gz. They're separate files (by chromosome) as shown here.

How could I create a dna.primary_assembly.fa.gz for canine genome that includes all chromosomes?

Thanks!

[GenoMax]

You should be able to cat the files together.

Answer 1

[Candice]

I've found the answer. It turns out the Readme in Ensemble says "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent."

Therefore, I can use the 'Canis_lupus_familiaris.ROS_Cfam_1.0.dna.topleve.fasta.gz' here