I'm trying to assemble metagenomic data that comes from termite guts. The sequences comes from SOLiD and no paired, so the reads are extremely short (25bp).

I have tried multiple assemblers (CLC, velvet, metavelvet, Meta-IDBA) but all produce few contigs (15 contigs, 1000bp average). The contig output is scarce considering the amount of raw data (5 Gpb).

Has anybody has any success in a task such as this?.


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    $\begingroup$ Not sure there is a lot you can do. 15 contigs of 10kb do seem awfully little, though. $\endgroup$ – Konrad Rudolph Aug 12 '12 at 22:45

This depends on your coverage and the number and relative proportion of species in the mixture. this seems unlikely to produce results unless the protocol biases the library (rRNA universal primers for instance.) I think at 25 bp sequences, even 30x coverage would not give full assembly sequences. Typically I believe 25 bp reads are only used to resequence close variants from similar or reference genomes.

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  • $\begingroup$ The protocol have not been biased, that would be the correct approach. I was just hoping for some new point of view. What do you think about comparative assemble against some other assembled metagenomic data set to compare?. Thanks $\endgroup$ – Martin Beracochea Aug 13 '12 at 12:41
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    $\begingroup$ Metagenomic data are tricky as novel organisms can't be identified. But since you are in a bit of a jam you might try blatting your 25mers against a library of a few thousand bacterial genomes (as many as you can get a hold of) and you would get some idea of the distribution of the species in your sample, though rigorous identification would be some work.... $\endgroup$ – shigeta Aug 14 '12 at 14:44
  • $\begingroup$ Thanks, I was planning to do something like that. I think I'm going to try against some of the known bacteria of termite guts. $\endgroup$ – Martin Beracochea Aug 14 '12 at 15:40
  • $\begingroup$ yup - better than nothing - plus the reads that do not form alignments will give you some idea of the novel content you are missing.... $\endgroup$ – shigeta Aug 15 '12 at 3:52

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