A simple nextflow pipeline for running kraken2 and bracken in a docker container
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Oct 8, 2025 - Nextflow
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bracken
Here are 9 public repositories matching this topic...
Creates a simple OTU table from Kraken2 report.
bioinformatics metagenomics python3 data-analysis metagenomic-analysis otu-table kraken2 bracken commmand-line
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Oct 15, 2024 - Python
A Shiny app for taxonomic abundance visualization
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May 6, 2024 - R
This script filters low abundant reads from Bracken outputs for downstream analyses
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Nov 30, 2021 - Shell
shotgun metagenomics pipeline to obtain relative abundances and pathway abundances
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Aug 6, 2025 - Nextflow
CMDB Quant Bio Project:Metagenomic pipeline using Kraken2 and Bracken to analyze gut microbiota differences across young, elderly, and centenarian cohorts.
taxonomy metagenomics microbiome aging microbiota microbiome-analysis buddy gut-microbiome kraken2 bracken dysbiosis centenarians microbial-diversity
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Dec 5, 2025 - R
Integrated 16S rRNA and shotgun metagenomic analysis of sourdough-based kvass fermentation. Explores how dietary fibre addition shapes microbial composition and metabolic potential using QIIME2, MetaPhlAn4, Kraken2, Kaiju, HUMAnN3, and DRAM2.0. Includes complete pipelines, metadata, and reproducible workflows implemented on HPC and local env
shell bash bioinformatics r nextflow shotgun hpc metagenomics dram kraken fermentation microbiome-analysis kaiju qiime2 bracken msc-dissertation humann3 metaphlan4 microbiome-metabolism kvass
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Oct 29, 2025 - Shell
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Jul 9, 2019 - Dockerfile
Here we discuss strategies and workflows to analyse metagenomics datasets
python r pipelines metagenomics kraken dada2 amplicon-sequencing qiime2 deblur bracken epi2me shotgun-metagenomics
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Dec 25, 2023
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