mapping scaffolds(bacteria) to a reference genome

Question

[noobiestar]

Hi, I am new to the world of bioinformatics. I have a bacterial genome in scaffolds. The bacterial genome is assembled into long scaffolds. I would like to map this to a reference genome of closely related bacteria. How should I do this? What software I can use?

Answer 1

[hugo.avila]

Hey ! There are many tools to do this, but I still think Mauve is the best (usability wise).

Take a look at the Mauve official website, they have a lot of tutorials on how to do genome comparisons and plots.

To get a close reference genome, you can download all complete genomes of the same bacterial species from RefSeq and use the pyani tool to choose the closest one. Another way is to just take the largest contig and use it as a query in the NCBI blast tool and choose the closest genome match as a reference, but this is not as accurate as using the entire genome with pyani. Pick a genome of reference (or more) and use Mauve to map and plot.

[noobiestar]

I have done BLAST and got the specific bacterial reference genome. Thanks for your advice with the mauve.

Answer 2

[GenoMax]

Answer depend on what you hope to get out of this analysis? Are you trying to estimate if your assembly is reasonably complete?

You could do one of the following:

1. Use minimap2 to map your assembly against the reference.
2. Use an aligner like lastz (LINK) that is designed for chromosome size sequences
3. Try mauve (LINK).

[noobiestar]

I am trying to figure out how close is the bacterial genome with reference genome. Thanks GenoMax

Answer 3

[pbioinf]

If that is your goal give fastANI"a try, very simply to use and low computational resource requirements. It will give a score for average nucleotide identity over the whole genome, not quite the same as aligning though!

https://github.com/ParBLiSS/FastANI