Snakemake statistics

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Snakemake specifications


Unique identifier OMICS_02299
Name Snakemake
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
BWA, SAMtools, BCFtools, Graphviz, PyYAML, Docutils
Maintained Yes




No version available



  • person_outline Johannes Köster

Publication for Snakemake

Snakemake citations


Nitrosospira sp. Govern Nitrous Oxide Emissions in a Tropical Soil Amended With Residues of Bioenergy Crop

Front Microbiol
PMCID: 5902487
PMID: 29692763
DOI: 10.3389/fmicb.2018.00674
call_split See protocol

[…] based on primer quality (≤ 2 errors), spacers (≤2 errors), and barcodes (≤1 error). Barcodes and primers were removed. Further, the sequences were processed using the UCLUST pipeline implemented in a Snakemake workflow which is available upon request (). In summary, the amoA-AOB sequences were truncated to 480 bp, clustered into 90% OTUs and singletons and chimeras were removed (). An OTU table wa […]


Discovery of physiological and cancer related regulators of 3′ UTR processing with KAPAC

Genome Biol
PMCID: 5875010
PMID: 29592812
DOI: 10.1186/s13059-018-1415-3

[…] e together with the estimated expression of poly(A) sites with sufficient evidence of usage.All scripts, intermediate steps, and analysis of the TCGA data sets were executed as workflows created with snakemake version 3.13.0 []. […]


Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities

Front Microbiol
PMCID: 5845876
PMID: 29563897
DOI: 10.3389/fmicb.2018.00294

[…] ic classification for each OTU was obtained by using the RDP Classifier version 2.10 using the bootstrap value of 80% and classification was done on full-length entries (). The pipeline was made with Snakemake () as available at DOI: (). This pipeline was also used for ITS with the following adjustments: (1) ITS2 regions where extracted using ITSx 1.0.11 (). ( […]


Improving saliva shotgun metagenomics by chemical host DNA depletion

PMCID: 5827986
PMID: 29482639
DOI: 10.1186/s40168-018-0426-3

[…] Demultiplexed sequences were processed using an in-house modular workflow employing Snakemake [] (, commit 1c393f4). First, reads were trimmed and quality filtered using Atropos v 1.1.5, a fork of Cutadapt []. Reads aligning to the host gen […]


Genome resolved metagenomics of sugarcane vinasse bacteria

Biotechnol Biofuels
PMCID: 5822648
PMID: 29483941
DOI: 10.1186/s13068-018-1036-9

[…] Bioinformatics processing was performed on a Linux server (Linux-3.13.0-76-generic-×86_64-with-Ubuntu-14.04-trusty) with 64 nodes and 250 GB RAM. Processing was performed in a Snakemake v3.7.1 workflow or with bash or Perl scripts (available upon request). The 18 shotgun metagenomes were checked for tag sequences and evaluated for statistics using FastQC v0.10.1 (Available […]


Growing old, yet staying young: The role of telomeres in bats’ exceptional longevity

Sci Adv
PMCID: 5810611
PMID: 29441358
DOI: 10.1126/sciadv.aao0926

[…] An automated workflow called OH-SNAP was constructed to run CodeML as implemented in the PAML package (). The workflow was designed using the Snakemake workflow management system () and was executed on a high-performance compute cluster. The workflow requires a species tree (described below), an alignment, a list of taxa contained within th […]


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Snakemake institution(s)
Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen and Paediatric Oncology, University Childrens Hospital, Essen, Germany

Snakemake reviews

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Samuel Lampa

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A top-quality software that is really helpful for low- to medium complexity workflows, especially where you might want to re-generate certain outputs based on updated inputs.

For really complex workflows, such as when involving multiple nested parameter sweeps and/or cross-validation constructs implemented in the workflow layer, it can get a bit complicated to figure out how to write that, and something more dataflow-like like NextFlow might be preferrable in such cases.

Fabien Pichon

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A useful pipeline generator in python that allows to create modules (rules) for each step. A little bit confusing at the beginning if one doesn't know make but very powerful at the end. An important point : Snakemake allows graphics workflow output.