Metagenomic profiling is broadly used to characterize microbial communities in animals, soil, water, etc. Gene of choice, 16S rRNA, has 9 variable regions (V1-V9), separated by conserved spaces. Resulting sequences are characterized for present species and diversity.
16S gene is 1500-1800 bp long. Comparing to Illumina, Nanopore gets the whole gene, greatly improving the resolution.
Characterize microbial communities in animals, soil, water, etc.
– Kraken is hash-based classifier. It's fast, but has high memory demand
– Centrifuge is FM-index-based classifier. It's slower, but much better on memory
– Pavian is modern tool for metagenomic visualization with per-sample and per-group statistics