All Published Workflows

4 workflows that have been reviewed and published

rna-seq-star-deseq2
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RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
public_trapseq
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Ribosome Profiling Data Analysis with Snakemake: public_riboseq Workflow
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
Gene expression profiling IHW PCAtools tximport Bowtie 2 DESeq2 kallisto pheatmap Quant Snakemake ggplot2 RColorBrewer Trim_Galore Sequence analysis
Free
8
blast-virome
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Virome taxonomic profiling using BLAST
public

public

Snakemake workflow for virome taxonomic profiling using BLAST. It's a subworkflow based on hivlab/discover-virome, uses assem...
Taxonomic classification Gene expression profiling Report RepeatMasker Snakemake taxonomic and functional annotation
Free
5
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
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