Interpretation of Euler-SR assembly (454 transcriptome)

[EMeyer]

Hi all,

We've recently completed a run of 454 sequences from the transcriptome of a reef-building coral, and I am in the process of attempting de novo assembly. Since it seems Euler-SR does better on this type of data than Newbler or CAP3, I am trying this software. But Im finding the output kind of hard to interpret.

Does anyone know of a good set of instructions for using this software? Anything specifically geared toward transcriptome, rather than genome, assembly would be especially useful.

On a more detailed note, does anyone know the following regarding the output of Euler-SR?

1. Is it possible to view singletons, and if so, where is that file?
2. Is there any output that describes the mapping of reads to contigs? (as, for example, was easily parsed from CAP3 output).
3. On what basis are reads excluded prior to assembly (e.g., for my test set of 2500 reads only 2477 were included at the beginning of assembly). And how can this behavior be adjusted if needed?

Thank for your any advice you might have,
-Eli

[sklages]

It might be interesting for you to have a look at MIRA for such kind of assemblies.

http://www.chevreux.org/projects_mira.html

Output alignment formats are CAF/gap4 and ACE.
It performs well on EST data (at least for what I have seen).

Cheers,
Sven

[EMeyer]

Thank you, I am impressed with the level of documentation for that package! I will give it a shot.

I didnt see a publication of the method itself. Do you know if there is one in preparation / in review?

[sklages]

There are two papers describing the package,

mira,
Chevreux, B., Wetter, T. and Suhai, S. (1999): Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.

miraEST,
Chevreux, B., Pfisterer, T., Drescher, B., Driesel, A. J., Müller, W. E., Wetter, T. and Suhai, S. (2004): Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs. Genome Research, 14(6)

I don't know if there is a publication in progress describing the forthcoming version 3 and/or the Illumina/SOLiD/454 support.

[EMeyer]

Thanks again. Its performing well on my dataset, giving a slightly larger average contig size than Newbler and a distribution of contigs that is both narrower and more normal. The big drawback I see at this point is that it gives me ~20% more contigs... this may be a good thing or a bad thing!

I'm still calculating the N50 and coverage for this assembly, but so far so good. One note, though -- on my dataset Mira performs very similarly to CAP3. (Mira is slightly better than CAP3 as judged by higher mean contig size and lower contig number).

Does that sound reasonable or does it sound like I'm doing something wrong?