All Published Workflows

5 workflows that have been reviewed and published

tourmaline
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Amplicon sequence processing workflow using QIIME 2 and Snakemake
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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
pore-c-snakemake
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Pore-C Snakemake Workflow for Processing and Analysis of Nanopore Sequencing Data
public

public

This pipeline manages a pore-c workflow starting from raw fastq files and converting them to standard file formats for use by...
raw sequence reads Alignment Feature table cooler BWA Pairix SAMtools Snakemake Sequence analysis
Free
32
qiime1-scripts
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Bash scripts for running QIIME 1.9 and a Snakemake workflow to automate it using singularity container images.
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MOTIVATION: Qiime 1.9 has reached the end of its life ycle and thus no longer maintained by its developers. Moreover, QIIM...
Sample annotation Gene functional annotation Feature table Cutadapt FastQC MultiQC PEAR PICRUSt2 seqkit Snakemake Trimmomatic Trim_Galore taxonomic and functional annotation
Free
30
taxprofiler
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Highly parallelised multi-taxonomic profiling of shotgun and long-read metagenomic data
public

public

nf-core/taxprofiler is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shot...
DNA sequence Gene expression profiling Feature table bracken porechop AdapterRemoval BBMap Bowtie 2 Centrifuge Diamond Falco fastp FastQC Filtlong Kaiju kraken2 KrakenUniq Krona MEGAN Metagenomic operational taxonomic units (mOTUs) MetaPhlAn Minimap2 MultiQC Nextflow SAMtools Malt Sequence analysis
Free
62
16s_biodiversity_biom
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Galaxy workflow that uses to convert the16S BIOM file to table and figures.
public

public

MetaDEGalaxy is a metagenomic analysis tool running on Galaxy platform. There is a number of scripts written in R and python ...
BIOM format Data Analysis Feature table DESeq2 Galaxy phyloseq WorkflowHub Biodiversity
Free