All Published Workflows

3 workflows that have been reviewed and published

mcclintock
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Meta-pipeline to identify transposable element insertions using next generation sequencing data
public

public

# INSTALL (Requires Conda and Mamba to be installed) git clone git@github.com:bergmanlab/mcclintock.git cd mcclintock mamba e...
FASTQ Sample ID Mapping Taxonomy ngs_te_mapper2 trim-galore RelocaTE2 Snakemake TEMP TEMP2 Whole genome sequencing
Free
16
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
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