Contig assembly question Mauve + RAST

[PhDiddy]

Hi All,

Wondering if you can help me out. I want to carry out comparative genome analysis of two bacterial species. For one of the species the annotated whole genome sequence is available on genbank. The other however is only available as contigs. I presume these contigs on genbank are not in order therefore I need to put them in the correct order.

I have tried using Mauve contig mover to do this but keep getting an error message and the run is terminated.

I have annotated the unordered contigs on RAST and can compare this to my reference genome (the species I have a complete genome sequence for)...does this now mean that my contigs are in the correct order or do I still need to put them in the correct order before uploading to RAST?

[sBeier]

What is the error message you get with Mauve contig mover? Most I got were memory issues, but not with ordering a bacterial genome. I solved those by using Mauve from the command line. This also is possible for the contig mover, and is described here: http://asap.ahabs.wisc.edu/mauve-ali...t-genomes.html

You could also just use progressiveMauve with your complete and contig reference, which will show you if the contigs are ordered or not. Because ordering the contigs after the other reference when they already have been ordered might result in loosing rearrangements.

[PhDiddy]

Thanks for the reply sBeier.

This the error message I am getting

"This application has requested the Runtime to terminate it in an unusual way.
Exited with error code: 3"

I will try with pregressiveMauve and see what happens

[sBeier]

What is directly before the error you quoted? Is this maybe "Storing raw sequence at [some path]"? Then, running Mauve from command line with higher memory might really help.

[PhDiddy]

Storing raw sequence at C:\Users\04550510\AppData\Local\Temp\rawC89.tmp

I'm a biologist...any bioinformatics or computer stuff absolutely baffles me!

[sBeier]

That looks a lot like a memory problem! With the command line from the link I gave above, "-Xmx500m" is where you set the memory used. You might have to change it appropriate for the hardware you are running it on. (the small m is "Mb" a g would be "Gb", so -Xmx1g would use 1 Gb of memory)

[PhDiddy]

You lost me at command line.

Is it that I need to increase the memory on my computer? I tried to open the Mauve.jar file to carry out the commandline function but it won't open as there's not enough memory.

Thanks so much for all your help

[PhDiddy]

Is there any other program I can use that will allow me to check if the contigs are in the right order?

[sBeier]

At the link I gave you the exact command on how to use the contig mover in command line is given. You might have to give the full path to your Mauve.jar. This is nothing you "open" by clicking on it and having something pop up, you need to type in the command in whatever representation of a terminal you have in your operating system. This is pretty hard to explain not knowing how much you know about computers or Mauve.
I meant not that you need to increase the memory on your computer, you need to increase the memory Java (and thus, Mauve) is allowed to use.