Efficient way to align assembled scaffolding to genome sequences from NCBI?

Question

[Kacper]

Hello all,

I am trying to identify a human functional homolog of a specific bacteria. I assembled and scaffolded the bacterial genome using SPAdes. I am now trying to align the assembled scaffolds onto a human-derived Lactobacillus species genome available on NCBI to identify a human-derived species who is a functional homolog of the assembled genome.

My question is, is there an efficient way which I can find a published genome which would be the closest to my assembly for the purpose of alignment?

I tried running a BLAST, however, I was told the query was too long. The total length I'm working with is 2.1 million bp.

Thank you in advance!

Answer 1

[Istvan Albert]

Find all lactobaccilus genomes put all genomes into a single file, run minimap2 on your contigs, and align against the combined genome.

Finally summarize the BAM with idxstats that will tell you which genome matches the most often.

Some from command line but you can also download the genomes from the NCBI website, see the FAQ

https://www.ncbi.nlm.nih.gov/genome/doc/ftpfaq/