bio-workflows-metagenomics-pipeline

You can automate end-to-end metagenomic analysis from raw FASTQ reads to taxonomic profiles using this pipeline. It handles quality control, host removal, taxonomic classification, and functional profiling to deliver publication-ready results with reduced manual steps.

The best way to profile microbial communities from shotgun metagenomics data is using an end-to-end pipeline that integrates QC, host removal, and taxonomic classification. This workflow processes raw reads to generate comprehensive taxonomic and functional profiles across your samples.

Yes, you can use Kraken2 and Bracken together for metagenomic taxonomic classification. This pipeline supports classifying taxa with Kraken2 and Bracken, or alternatively MetaPhlAn, allowing you to choose the appropriate tool for your microbial community profiling needs.

Yes, this metagenomics pipeline supports functional profiling with HUMAnN. It integrates HUMAnN to profile microbial functions and compare pathways, generating ready-to-visualize results that complement the taxonomic profiles produced by Kraken2, Bracken, or MetaPhlAn.

You remove host contamination from shotgun metagenomics reads by applying Bowtie2 within this pipeline. It automates host removal as a core preprocessing step after initial quality control with fastp, ensuring clean reads for downstream taxonomic and functional profiling.

Yes, you need to adjust parameters for different shotgun metagenomics samples. While the pipeline provides recommended defaults for tools like fastp, Kraken2, and HUMAnN, sample-specific adjustments are supported to optimize QC, host removal, and profiling accuracy for your dataset.