mauve alignment results meaning
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2.0 years ago
langziv ▴ 20

Hi.

The alignment representation makes me think the 2 aligned genomes have no matching sequences, since I haven't seen such results when I searched for mauve results.

The alignment results image:

These two genomes are from 2 distinct samples that are of the same organism, so they are expected to have many matches.

mauve progressiveMauve • 1.1k views
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Is that an assembly? If memory serves, the red bars demarcate discontinuous boundaries between sequences.

That looks like a LOT of contigs - is this normal for your organism? If not, are you sure your assemblies are good?

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It is an assembly. That's the amount of contigs we got after using programs such as cutadat, trimmomatic and bwa, among others. I don't know if it's normal or not. My PI seems ok with that. She's the experienced one in doing assemblies.

All the programs we used ran fine. There were no errors. Maybe there's something wrong about the raw data. We didn't do the sequencing part. We got it from another lab.

The results don't indicate about any similarities between the assemblies, right?

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All the programs we used ran fine. There were no errors.

This does not mean that the results are reasonable or even correct. As @Joe said you have not mentioned an assembler yet. What is the size of this genome? Perhaps mauve is not the right program to use.

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The assembler we used was IDBA-UD. The genome size is about 1.4E9 (9 digits) bp. I read that the latest mauve version is suited for large genomes as well.

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That is a large genome. Based on results you are observing perhaps you should try something else. musgy (LINK) is an older tool that is recommended for this purpose. I found GS-ALIGN (LINK), MUMmer4 (LINK), SibeliaZ (LINK) seem to be recent options.

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Sorry for the silly question, but you actually ran the mauve/progressiveMauve algorithm after reading the sequences in to the software right?

If so, then yes, that indicates little to no similarity as far as I can tell. If you are confident in the assembly process (though you haven't actually mentioned an assembler, so I would double check this too), then the raw reads are probably at issue which has led to a poor assembly.

You may want to screen the reads and make sure there is little to no contamination and that the library quality is decent.

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That was a long time ago. I don't remember. Eventually I used another program.