Estimation Of The Probability Of Chimera In A Metagenomic Assembly?

Question

[Manu Prestat]

Does anybody know how to estimate the probability/number of chimera in a metagenomic assembly?

(I don't talk about PCR generated chimera, only assembly).

Answer 1

[Manu Prestat]

To go deeper in the problem, to have a strongly accurate estimation, one would need to have a good estimation of the distribution of species and to know the size of the genomes of these species. This is actually a fundamental open question, especially in most diverse biomes (soil, gut, etc). But I just learnt that, to have at least an insight of chimera detection, it is relevant to use coverage information statistics. For instance, if in one contig the variance of nt coverage is high, or the median is much more different from the mean, the contig may be chimeric.