Hi SEQanswers experts,
I've used megan extensively to taxonomically classify reads from metagenomes which is, according to the initial publication, one of the main reasons the software exists. However, I wonder if it also suitable to classify genes from assembled metagenome contigs - or even whole contigs. I am only interested in a very high level (Domain) classification to estimate the contribution of archaea, bacteria, eukaryotes, and virusses/phages to the metagenome. Since megan only uses the blast result files there shouldn't be a technical problem but I am worried about the theoretical concepts behind the algorithms (e.g. LCA), will megan still yield unbiased & reliable results?
If so, I would appreciate advice for which blast[n|p] and megan parameters in order to yield best results for gene or contig blasts.
Lastly if megan turns out to be not applicable to my problem, do you know about software that would be better suited?
Thanks in advance
I've used megan extensively to taxonomically classify reads from metagenomes which is, according to the initial publication, one of the main reasons the software exists. However, I wonder if it also suitable to classify genes from assembled metagenome contigs - or even whole contigs. I am only interested in a very high level (Domain) classification to estimate the contribution of archaea, bacteria, eukaryotes, and virusses/phages to the metagenome. Since megan only uses the blast result files there shouldn't be a technical problem but I am worried about the theoretical concepts behind the algorithms (e.g. LCA), will megan still yield unbiased & reliable results?
If so, I would appreciate advice for which blast[n|p] and megan parameters in order to yield best results for gene or contig blasts.
Lastly if megan turns out to be not applicable to my problem, do you know about software that would be better suited?
Thanks in advance
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