metagenomics

You can perform shotgun metagenomics analysis with host read depletion by running an integrated workflow that applies host-depletion-aware QC to decontaminate reads. It then identifies and quantifies taxa while controlling for host reads to produce taxonomic profiles.

The best way to profile taxonomic composition from shotgun metagenomics data is using Kraken2 as the primary profiler. This workflow generates reproducible, cohort-ready output tables suitable for multi-sample comparisons across diverse microbiomes like gut, soil, or aquatic samples.

Yes, you can infer functional pathways and perform AMR detection from shotgun metagenomics data. The workflow supports functional profiling and AMR follow-up for interpretation and reporting, using Humann as an optional component alongside the primary profiler.

Yes, this metagenomics workflow supports cohort-level comparative analyses across multiple samples. It produces reproducible, cohort-ready output tables from decontaminated reads, enabling multi-sample comparisons for projects analyzing diverse microbiomes such as gut, soil, or environmental samples.

You need host depletion in microbiome taxonomic profiling when working with samples heavily contaminated with host reads. The workflow employs host-depletion-aware QC to decontaminate reads, ensuring accurate taxonomic and functional profiling from shotgun metagenomics data.