All Published Workflows

5 workflows that have been reviewed and published

foodme
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A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
public

public

FooDMe is a reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special fo...
JSON paired sequencing data Filtering Quality control report Biopython BLAST Consensus Cutadapt fastp Krona Pandas seqtk Snakemake DT htmltools tidyverse PyYAML taxidTools Taxonomy
Free
60
taxonomic_profiling_pipeline
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taxonomic_profiling_pipeline
public

public

This pipeline was developed using the Snakemake workflow management system You would need to have the Snakefile, the en...
FASTQ Sample annotation Sequencing quality control Taxonomic classification fastp FastQC Kraken kraken2 Krona MultiQC Snakemake Taxonomy
Free
11
hull_microbiome_cluster_workflow
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Snakemake workflow for microbiome research cluster analysis using fastp, Kraken2, and BIOM.
public

public

A Snakemake workflow to analyse long read human microbiome data with steps for general quality control and taxonomy assignmen...
Expression data Sequencing quality control Taxonomy kraken-biom fastp kraken2 seqkit Snakemake Taxonomy
Free
8
samba-standardized-and-automated-metabarcoding-ana
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SAMBA: Standardized and Automated MetaBarcoding Analyses workflow
public

public

SAMBA is a FAIR scalable workflow integrating, into a unique tool, state-of-the-art bioinformatics and statistical methods to...
FASTQ JSON raw sequence reads Statistical calculation Report Cutadapt DESeq2 Minimap2 PICRUSt2 QIIME2.0 SAMtools seqtk subSeq ggplot2 Taxonomy
Free
30
1-plant-virus-detection-with-kraken2-se
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Plant virus detection with kraken2 (SE)
public

public

Metagenomic dataset taxonomic classification using kraken2
Galaxy kraken2 Krona WorkflowHub Plant biology Taxonomy
Free