Hello,
I would like to know what are your thoughts on using read-based and contig-based taxonomy as implemented in tools similar to Kraken and Centrifuge.
Would read-based taxonomy be different from contig-based results? When should I do read-based over contig-based taxonomy (and vice-versa?)
Thanks for your input!
Angelo,
You should use both ways. Read-based taxonomy will identify relatively similar taxonomic units (good for well-known bacteria), but contig-based comparison will give you more information about evolution and distant relatives of your microbes.
Regards
Alex
I depends to some degree on what type of information you want from your data. If you want to know the relative level or number of cells of one taxon vs another, read-based methods will do better. If you want to know more about the diversity of taxa present but not so interested in what level of each, contig-based methods may be better. If you want to know which species/taxa are carrying out various functions in the sample (fixing nitrogen, producing alcohol, etc) you may want to use only the reads or contigs from the enzymes involved in those functions.
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