All Published Workflows

27 workflows that have been reviewed and published

tourmaline
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Amplicon sequence processing workflow using QIIME 2 and Snakemake
public

public

Tourmaline is an amplicon sequence processing workflow for Illumina sequence data that uses QIIME 2 and the software pack...
CSV Database metadata Analysis Feature table clustalo fasttree CLICK MAFFT API (EBI) Pandas QIIME2.0 Snakemake matplotlib numpy seaborn tabulate Metagenomic sequencing
Free
57
unite-train
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🍄 Qiime2 ITS classifiers for the UNITE database
public

public

A pipeline to build Qiime2 taxonomy classifiers for the UNITE database . Set up: Install Mambaforge and c...
QIIME2.0 Snakemake
Free
4
cascabel
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Automated pipeline for amplicon sequence analysis
public

public

Cascabel is a pipeline designed to run amplicon sequence analysis across single or multiple read libraries. The objective ...
format fasttree BLAST Cutadapt mothur PEAR QIIME2.0 Snakemake Swarm VSEARCH benchmark-utils
Free
153
snakemake-workflow-qiime2
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Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2
public

public

This workflow performs microbiome analysis using QIIME2 and PICRUSt2 for functional annotation. Functional annotation is only...
Cutadapt MAFFT API (EBI) PICRUSt2 QIIME2.0 Snakemake VSEARCH
Free
43
microbiome16s_pipeline
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Reproducible Scalable Pipeline For Amplicon-based Metagenomics (RSP4ABM) is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
public

public

This is a comprehensive pipeline for amplicon-based metagenomics integrating in a Snakemake workflow the best functions of ...
dada2 biomformat Biopython Biostrings Consensus Cutadapt DECIPHER edgeR FastQC Krona metagenomeSeq MultiQC Pandas PANDAseq phyloseq PICRUSt2 QIIME2.0 Snakemake SRA VSEARCH data.table dplyr ggplot2 magrittr plyr RColorBrewer reshape2 stringr tibble tidyr vegan
Free
97
snakecharmer
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Amplicon data processing workflows for diversity analysis
public

public

This software makes use of the workflow management system Snakemake to build and integrate different amplicon workflows a...
JSON Biopython Consensus Cutadapt FastQC ITSx MultiQC QIIME2.0 SAMtools Snakemake VSEARCH stringr yaml PyYAML utils
Free
83
16s
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16S pipeline using qiime2 created with snakemake
public

public

Qiime2 workflow for 16S analysis created with snakemake. Ann-Kathrin Brüggemann (@AKBrueggemann) Thomas Battenfeld (@...
Bowtie 2 Cutadapt FastQC MultiQC Pandas QIIME2.0 SAMtools Snakemake VSEARCH matplotlib numpy oyaml prettytable seaborn pyLabLib
Free
152
avengers-assemble
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Microbiome Analysis Workflow based on a qiime2
public

public

This repository contains the analysis workflow for Debelius et al (doi: 10.1101/2021.03.23.436606 ). The analysis was don...
Cutadapt Pandas QIIME2.0 Snakemake VSEARCH argparser vegan numpy regex scikit-bio Function analysis
Free
46
qiime_pipeline
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CGR's QIIME microbiome pipeline
public

public

This is the Cancer Genomics Research Laboratory's (CGR) microbiome analysis pipeline. This pipeline utilizes QIIME2 to cl...
QIIME2.0 Snakemake
Free
40
biof501termproject
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Term Project for BIOF 501 UBC
public

public

Background and hypothesis Dependencies Workflow Usage Input Expected output ...
FastQC MultiQC QIIME2.0 Snakemake
Free
10
nanoclass
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NanoClass: A Taxonomic Meta-Classifier for Oxford Nanopore Amplicon Sequencing Data
public

public

NanoClass is a taxonomic meta-classifier for 16S/18S amplicon sequencing data generated with the Oxford Nanopore MinION. With...
nanofilt nanostat porechop spingo dada2 Biopython BLAST Centrifuge Consensus DECIPHER kraken2 MAPseq Minimap2 mothur phyloseq QIIME2.0 SAMtools seqtk Snakemake ggplot2 seqinr tidyr vroom Sequence analysis
Free
68
env-diversity
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Amplicon data processing workflows for diversity analysis
public

public

This software makes use of the workflow management system Snakemake to build and integrate different amplicon workflows a...
JSON Biopython Consensus Cutadapt FastQC ITSx MultiQC QIIME2.0 SAMtools Snakemake VSEARCH stringr yaml PyYAML utils
Free
83