Create a new reference genome with denovo assembly and standard reference with long read data?

Question

[eorr]

Hi,

I have WGS PacBio Long read data of a mouse cell line and a denovo genome assembly was performed by the sequencing center via SMRT link analysis (I don't have much more information as far as programs, parameters etc.). The assembly produced ~3000 contigs. I would like to somehow compare the denovo genome to the GRCm39 reference genome to see where the contigs are mapping to each chromosome. Any thoughts? Thanks in advance!

-Emily

[GenoMax]

Start by using minimap2 (LINK) to align the contigs you have to the existing assembly. There are other tools like lastz (LINK) that can also align large contigs. But using minimap2/samtools can allow you to generate BAM format files that you can easily visualize using IGV (LINK).

Answer 1

[gconcepcion]

minimap2 would be your best bet.

https://github.com/lh3/minimap2

in short, you would run something like this:

$ minimap2 -ax asm5 reference.fasta assembly_contigs.fasta > output.sam

https://github.com/lh3/minimap2?tab=readme-ov-file#full-genome

You could then view the alignments in IGV https://igv.org/doc/desktop/