What is the difference between the taxonomy classification and binning in metagenomic?

Question

[QuotoAstro]

Hi, I am doing a survey on metagenomic binning, and the difference between taxonomy classification and binning makes me confuse, can anybody help me?

According to the wikipedia, binning is the process of grouping reads or contigs and assigning them to individual genome, and classification(NCBI standard) which can be organized as a tree, give every sample(or genome) a taxa(or tag).

And now, with tools like Kraken or centrifuger, we can classify the reads to the species. What if I give a metagenomic which organisms that we all know, is not binning just classification?

Answer 1

[Jess]

Binning and taxonomic classification are two different processes. Similarly to what you mentioned, binning is where you will group/cluster together sequences (reads) which are predicted to be part of a single genome. The binning tools I have used (MetaBAT for example) in the past do not assign taxonomy to the bins, you get and output of e.g. 'bin.300' and within is a fasta alignment.

There are then tools you can use for taxonomic classification of those bins. Like you said, you can use Kraken or Centrifuge for this. However, when you say 'classify the reads', this suggests you are using these tools for you metagenomic reads and not your bins. I believe you can use these tools for classification of either reads or bins but they will tell you different things about your data.

Hope this helps and let me know if anything is not clear.

[pbioinf]

Good answer, maybe it would be good to add that there are binning pipelines that do add taxonomic classifications to their output bins.

[QuotoAstro]

Thanks for your reply, and that really help me!