All Published Workflows

38 workflows that have been reviewed and published

atlas
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ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
metagem
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:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
public

public

Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
JSON raw sequence reads Genome assembly Quality control report prodigal MEGAHIT BWA CheckM fastp kallisto MaxBin memote MetaBAT 2 metaprokka MetaWRAP Quant Roary SAMtools Snakemake SqueezeMeta CONCOCT carve gtdbtk smetana metagenomics
Free
35
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
lathe
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A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
public

public

A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
bacterial Base-calling Sample annotation mummer2circos tabix BCFtools BEDTools BWA CANU Consensus Flye GUPPY Medaka Minimap2 NanoPlot pilon Racon SAMtools Snakemake pysam metagenomics
Free
39
phanta
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Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
public

public

Workflow figure created on BioRender.com. Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut ...
bacterial Labeled quantification Scatter plot plotting Plot bracken kraken2 Pandas Snakemake stringr numpy metagenomics
Free
23
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
strainsifter
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A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
public

public

A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...
bacterial Phylogenetic analysis Phylogenetic tree fasttree BamTools BEDTools BWA Consensus ggtree SAMtools Snakemake ggplot2 phangorn metagenomics
Free
22
eukrhythmic
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A metatranscriptomic pipeline optimized for the study of microeukaryotes.
public

public

This README file is a brief introduction to eukrhythmic . For more detailed information, please visit the readthedo...
FASTQ Sample annotation Transcriptome assembly Quality control report BBMap BEDTools cd-hit Quant QUAST Salmon Snakemake TransDecoder metagenomics
Free
27
kount
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Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.
public

public

Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data. KOunt is a Snakemake pipeline that cal...
Pathway ID (KEGG) Quantification Quality control report prodigal MEGAHIT BEDTools BWA cd-hit Diamond fastp kallisto MMseqs Quant SAMtools seqtk Snakemake subSeq kofam_scan oschmod metagenomics
Free
41
tara-euk-metag
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Snakemake workflow for analysis of Tara Euk Metagenomes
public

public

Create a conda environment for the running of the pipeline: conda env create --name snakemake-tara-euk --file environment.yaml
Feature table Analysis Report eukrep prodigal MEGAHIT BWA CoverM FastQC MetaBAT 2 MultiQC SAMtools Snakemake Trimmomatic CONCOCT metagenomics
Free
25
2021-metapangenome-example
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Metapangenomics Workflow for Amino Acid K-mers Comparison
public

public

This repository implements an example workflow for performing metapangenomics using amino acid k-mers, and compares this pipe...
Sequence comparison MEGAHIT BBMap Bowtie 2 BWA cd-hit fastp MetaBAT 2 metaprokka Pagoo Pandas SAMtools seqtk Snakemake subSeq aplot dplyr ggplot2 purrr readr tidyr lxml metagenomics
Free
117
snakemake-metagenomics
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Snakemake workflow for metagenomic analysis of rumen samples from sheep
public

public

Snakemake workflow for metagenomic analysis of rumen samples from sheep
Sample annotation Analysis Report bracken FastQC humann kraken2 MultiQC seqkit Snakemake metagenomics
Free
18