Top workflows by tests

snakemake-workflows

rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

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Updated: 2025-09-05 Release: v3.0.1formatting: passedlinting: passed

345 stars

12 watchers

KasperSkytte

snakemake_usearch

Simple snakemake workflow based on the usearch11 SOP

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Updated: 2025-09-05 Release: v1.1.2formatting: passedlinting: passed

0 stars

1 watchers

EloiseIsobelPearce

snakemake-example

During my time at Esox Biologics, I became confident using Snakemake to create streamlined MAG-assem…

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Updated: 2025-09-04 Release: Noneformatting: passedlinting: passed

0 stars

0 watchers

calliope-project

module_geo_boundaries

A module to create arbitrary regional boundary datasets for energy systems modelling

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Updated: 2025-09-02 Release: v0.1.4formatting: passedlinting: passed

0 stars

2 watchers

vjcitn

rnaseqSnake

demonstration snakemake repo for use with rnaseqGene workflow of Bioconductor

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Updated: 2025-09-01 Release: Noneformatting: passedlinting: passed

0 stars

0 watchers

IKIM-Essen

metagenomics_res

No description available.

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Updated: 2025-08-28 Release: Noneformatting: passedlinting: passed

1 stars

1 watchers

zavolanlab

mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries…

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Updated: 2025-08-22 Release: v0.9.1formatting: passedlinting: passed

6 stars

4 watchers

TidballLab

SNP-Cas13d-Selector

No description available.

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Updated: 2025-08-21 Release: Noneformatting: passedlinting: passed

0 stars

0 watchers

delpropo

TidballLab-SNP-Cas13d-Selector

A flexible pipeline for identifying heterozygous SNPs in CDS and 3′ UTR regions and selecting the op…

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Updated: 2025-08-21 Release: Noneformatting: passedlinting: passed

0 stars

0 watchers

IKIM-Essen

QC_pre_NextSeq

Workflow for short quality control of MiSeq sequencing data before sequencing on high throughput dev…

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Updated: 2025-08-14 Release: Noneformatting: passedlinting: passed

0 stars

1 watchers

MPUSP

snakemake-simple-mapping

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

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Updated: 2025-08-12 Release: v1.2.0formatting: passedlinting: passed

1 stars

1 watchers

StergachisLab

IsoSeq_smk

Pipeline for MAS-Seq processing

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Updated: 2025-08-09 Release: Noneformatting: passedlinting: passed

7 stars

5 watchers

niekwit

methyl-seq

Snakemake workflow for bisulphite sequencing analysis

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Updated: 2025-08-05 Release: Noneformatting: passedlinting: passed

0 stars

0 watchers

snakemake-workflows

rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

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Updated: 2025-08-04 Release: v3.0.0formatting: passedlinting: passed

68 stars

4 watchers

snakemake-workflows

dna-seq-benchmark

A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM…

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Updated: 2025-08-01 Release: v1.13.0formatting: passedlinting: passed

12 stars

1 watchers