Taxonomic Profiling of Shotgun Metagenomes
16S vs Shotgun
| Feature | 16S amplicon | Shotgun | |---|---|---| | Resolution | Genus level | Species/strain level | | Functional info | No | Yes | | Host contamination | N/A | Major issue | | Cost/sample | ~$30-80 | ~$200-500 |
Host Read Removal
Tool: Bowtie2 with --un-conc-gz to output non-host read pairs.
Typical host contamination: gut 1-10%, skin 10-30%, BAL 40-80%, blood 60-95%.
Kraken2 Classification
Assigns reads to LCA of a
[Description truncada. Veja o README completo no GitHub.]