All Published Workflows

7 workflows that have been reviewed and published

rna_seq_pipeline
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Global workflow: RNA Sequencing Analysis Pipeline with Miniconda and Snakemake
public

public

First step : Data cleaning (Optionnal) Second step : Get references files (reference genome, transcriptome) Then: Differe...
Sequence analysis biomaRt PCAtools BBMap Cutadapt DESeq2 FeatureCounts gffread Quant Salmon SAMtools Snakemake STAR devtools docopt ggplot2 tidyverse RNA-Seq
Free
40
rnaseq
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RNA-Seq Analysis Workflow for Single-End Data using qproject
public

public

RNA-Seq workflow for single-end data. The workflow can be downloaded and run on a cluster environment using the tool qproject...
Sequence analysis Bowtie 2 Cutadapt FastQC HTSeq htseqcount Pandas SAMtools Snakemake RNA-Seq
Free
23
variantcallingwithsnakemake
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Genome Re-sequencing Analysis Snakemake Workflow: De-novo and Variant Calling Modes
public

public

This Snakemake workflow is for analysing genome re-sequencing experiments. It features 2 modes. The **de-novo** mode is used ...
JSON Sequence analysis Variant calling seqhax AdapterRemoval BCFtools BWA FreeBayes kWIP Mash QualiMap SAMtools Snakemake snpEff rgl matplotlib numpy pysam tqdm DNA Sequence analysis
Free
41
medipipe
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MEDIPIPE: (cf)MeDIP-seq Data QC and Analysis Pipeline (v1.1.0)
public

public

The MEDIPIPE is designed for automated end-to-end quality control (QC) and analysis of (cf)MeDIP-seq data. The pipeline start...
File format name Sequence analysis tabix umi_tools BEDTools FastQC Picard SAMtools Snakemake Data quality management
Free
33
rnafusion
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RNA-seq analysis pipeline for detection gene-fusions
public

public

nf-core/rnafusion is a bioinformatics best-practice analysis pipeline for RNA sequencing analysis pipeline with curated li...
Sequence variations Sequence analysis Data gatk squid Arriba Bedops fastp FastQC gtftogenepred kallisto MultiQC Nextflow Picard Pizzly QualiMap Quant SAMtools STAR STAR-Fusion StringTie RNA-Seq Sequence analysis
Free
85
scrnaseq
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A single-cell RNAseq pipeline for 10X genomics data
public

public

nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data....
Sequence Sequence analysis Data simpleaf alevinQC FastQC gffread kallisto MultiQC Quant Salmon SAMtools STAR UniverSC kallistobustools Genomics Sequence analysis
Free
36
sars-cov-2-pe-illumina-artic-ivar-analysis-sars-co
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COVID-19 sequence analysis on Illumina Amplicon PE data
public

public

COVID-19 sequence analysis on Illumina Amplicon PE data sars-cov-2-pe-illumina-artic-ivar-analysis/SARS-COV-2-ILLUMINA-AMPLIC...
File format name Sequence Sequence analysis Sample ID nextclade usher BWA fastp Galaxy iVar MultiQC nextstrain.org Pangolin QualiMap SAMtools snpEff WorkflowHub Sequence analysis
Free