Align bacterial contigs to a reference genome and visualize the alignment.

Question

[rikki.frederiksen]

Hi,

I have a FASTA file containing contigs, which I want to align to a bacterial reference genome, and then visualize the alignment. Should be a simple task, but I have failed to install either Artemis, Mauve or Alvis in my linux OS. If anyone knows of an installable and intuitive program (either command line or GUI) for doing such an alignment, then please let me know.

Best, Rikki

Answer 1

[Mensur Dlakic]

I think you may be going at this the wrong way. Rather than rejecting proven programs because you can't install them and asking for programs you can install (how do we know what you can install?), it may be be better to ask for help in installing those programs.

But since you asked, mummer is another program for genome alignments.

[hugo.avila]

I agree with @Mensur Dlakic keep trying to install your first alternatives. Send us the log of your failed attempts and we will try to help you. Installing programs is almost always a pain, which is why I strongly recommend you to use Conda (miniconda). Conda is really easy to set up and I think you can install all the programs you mentioned above with it in just one line of code in a virtual environment without sudo.

This is the miniconda page look for a tutorial on youtube if you need it, but basically just download the executable and then run its installation script.

By the way, I had good results with this tool, try it if you want: medusa. It can be run from a web browser or as a standalone tool (which you can easily install via conda).

[rikki.frederiksen]

Thanks a lot Hugo,

I will install miniconda right away, and post the logs if my attempts fail.

Best.

[rikki.frederiksen]

Thanks Mensur,

I have meticulously followed the installation instructions for these tools. But yes, perhaps I should instead have asked if anyone would have a working script for installing any of these programs in Linux. If I fail to install MUMmer as well, I will follow your advice :). Thanks again.

Best, Rikki

[rikki.frederiksen]

Dear Mensur,

I eventually managed to install mummer4 and to generate a figure of the alignment between my reference "GCF_000006765.1_ASM676v1_genomic.fasta" and my contigs "pseudo_contig.fasta" using the following code as per the manual:

 ./mummer -mum -b -c GCF_000006765.1_ASM676v1_genomic.fasta pseudo_contig.fasta > mummer.mums
 mummerplot -postscript -p mummer mummer.mums

I was expecting a dotplot as shown in the manual, but instead the output is a graph more resembling a percent identity plot, except that it actually has the reference on the x-axis (and not percent identity) and query on the y-axis:

Does it seem like I have done something wrong, or is there a way to interpret this figure?

Best, Rikki

[GenoMax]

Have you tried to do mums one contig at a time? Based on your description it sounds like you have more than one contig.

[rikki.frederiksen]

Thanks GenoMax. What would the purpose be of aligning with only a single contig? The manual claims to be able to handle assembly files with 1000s of contigs, so this shouldn't be a limitation. Best, Rikki

[GenoMax]

It may produce a simpler graph than the one you have above that can help you understand how that contig relates to the genome.