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 11 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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Feb 11, 2026 - 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
A reproducible QIIME 2 MOSHPIT pipeline that assembles, bins, dereplicates and taxonomically classifies whole‑metagenome data. Includes MEGAHIT assembly, MetaBAT 2 binning, BUSCO quality control, Sourmash dereplication and Kraken 2/Bracken abundance estimation. Ideal for microbial‑ecology, functional‑genomics and strain‑level profiling studies.
mag assembly metagenomics binning microbial-ecology qiime2 busco kraken2 bracken megahit shotgun-sequencing moshipt metabat2
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Jun 5, 2026 - Python
Multi-omics characterization of the oral-gut-brain axis in Parkinson's disease using shotgun metagenomics, microbial biomarker discovery, and machine learning.
machine-learning bioinformatics nextflow metagenomics xgboost network-analysis parkinsons-disease microbiome-analysis wgs-data gut-microbiome kraken2 bracken shotgun-metagenomics humann3 oral-microbiome biomarker-prediction microbial-biomarker oral-gut-brainaxis
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Jun 30, 2026 - HTML
Integrated 16S + shotgun metagenomics workflow for kvass fermentation (QIIME2, MetaPhlAn4, Kraken2, HUMAnN3, DRAM2) with reproducible outputs.
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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Feb 28, 2026 - Shell
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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Jul 9, 2019 - Dockerfile
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