All Published Workflows

3 workflows that have been reviewed and published

kraken2_classification
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Snakemake workflow for metagenomic classification with Kraken2
public

public

A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysi...
Database ID Taxonomic classification Plot bracken kraken-biom cmapR ALDEx2 Kraken kraken2 Krona Pandas Snakemake ggplot2 ggpubr RColorBrewer reshape2 vegan metagenomics
Free
18
metax_bakeoff_2019
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Metagenomic Taxonomic Classification Benchmarking Workflow
public

public

Metagenomic taxonomic classification benchmarking This package is contains snakemake workflows, a jupyter notebook and a pyth...
raw sequence reads Taxonomic classification Taxonomy bracken prophyle BLAST Centrifuge Diamond FastQC Kaiju Kraken kraken2 metaX Picard SAMtools seqtk Snakemake ncbi-genome-download metagenomics
Free
78
gvclass
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gvclass: Taxonomic Classification of Giant Viruses and MAGs
public

public

version 0.9.4 March 7, 2023 Giant viruses are abundant and diverse and frequently found in environmental microbiomes. gvclas...
Taxonomic classification fasttree prodigal Biopython BLAST CLICK Diamond hmmsearch (genouest) MAFFT API (EBI) Pandas Snakemake trimAl ete3 sklearn viral-genomics
Free
26