All Published Workflows
105 workflows that have been reviewed and published
![chipseq](https://media.bioworkflows.com/bioworkflows/public_preview/d5a1471bc769b0779a03b6e92fa2cd39daf943eed9df28474a728f4f3f6602cb.jpg)
ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).
This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
![stag-mwc](https://media.bioworkflows.com/bioworkflows/public_preview/d1aa95ef58e060110d23438f69ce196d8016620c23b2a73a1b07b340a634f0b0.jpg)
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
![pyflow-rnaseq](https://media.bioworkflows.com/bioworkflows/public_preview/88cb5e4487296b82d57088487a14e8b60d61a131ad56f2ddedff38fe8e601de6.jpg)
RNAseq pipeline based on snakemake
If you use this pipeline, please cite:
If inputs are fastq files:
The output folder will be suffixed by _fq
I...
![nbis-meta](https://media.bioworkflows.com/bioworkflows/public_preview/a313d869a5ece3cb72c146dd91f5ddf1cba1017dc12325245ea497335fce687c.jpg)
A snakemake workflow for metagenomic projects
A workflow for metagenomic projects A snakemake workflow for
paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap
prodigal
MEGAHIT
Biopython
BLAST
Bowtie 2
Centrifuge
CheckM
contigtax
Cutadapt
edgeR
eggNOG-mapper v2
FastANI
FastQC
FeatureCounts
Infernal cmscan (EBI)
kraken2
Krona
MaxBin
MetaBAT 2
metagenomeSeq
MetaPhlAn
metaspades
MultiQC
Pandas
Picard
SAMtools
seqtk
Snakemake
SortMeRNA
SqueezeMeta
Trimmomatic
Trnascan-SE
CONCOCT
common
gtdbtk
networkx
numpy
RGI
![hribo](https://media.bioworkflows.com/bioworkflows/public_preview/b9ccf3ffc6327aecb53559c34b52241affac86b26d9412bb52f9e5ac8389e542.jpg)
HRIBO: High-throughput annotation by Ribo-seq workflow for analyzing bacterial Ribo-seq data
We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of ...
![marky-coco](https://media.bioworkflows.com/bioworkflows/public_preview/a0bc4bc114aa88eaa25439bc1a4f844b16739affb06a73cc86cb204e82b70dc5.jpg)
Ready-to-use pipeline to detect, count and identify the hgcAB genes, involved in mercury methylation, from metagenomes
Marky-coco is a ready-to-use pipeline to detect and identify hgcAB genes from raw paired-end and single end fastq files. This...
![iclip](https://media.bioworkflows.com/bioworkflows/public_preview/324149cde88d7b7891ec8f39e8317d22bf6758a44a8f04a911094f48ff7af346.jpg)
![rna](https://media.bioworkflows.com/bioworkflows/public_preview/a10a8e764d26f8eab89176f1f0e6ddc6a4126f4cb2cdf4d9c20455bb9655ae5a.jpg)
![iclip](https://media.bioworkflows.com/bioworkflows/public_preview/1adbb3b9ea40dc6fc0b539fdaecb994b11d3e40e7c71d6be3e516e1868f4ae49.jpg)
![rna_seq_pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/24b88655a741e26d22ec883dedcc244ca4b7ca4eef4ac9e43464336d981101b4.jpg)
Global workflow: RNA Sequencing Analysis Pipeline with Miniconda and Snakemake
First step : Data cleaning (Optionnal) Second step : Get references files (reference genome, transcriptome) Then:
Differe...
![snakemake_hisat-deseq](https://media.bioworkflows.com/bioworkflows/public_preview/03b8fbf829e3dcf86d4f4df779e9f2898c42d135ee00fda1c52908895435b92e.jpg)
A Snakemake pipeline to analyse RNA-Seq reads
A snakemake pipeline for the analysis of RNA-seq data that makes use of hisat2 and DESeq2 . To align, count, normaliz...
![snake_hisat](https://media.bioworkflows.com/bioworkflows/public_preview/2e78f84a13238dc596194b8e23930d1eb73483a23aead475a2b37d9c7681a886.jpg)
RNA-Seq Analysis Workflow with HISAT2 Aligner
Workflow for RNAseq, using hisat2 aligner
wget https://cloud.biohpc.swmed.edu/index.php/s/grch38/download
mv download grch39....