Snakemake protocols

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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



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  • person_outline Johannes Köster <>

Publication for Snakemake

Snakemake in pipelines

PMCID: 5437120
PMID: 28579987
DOI: 10.3389/fimmu.2017.00547

[…] called “bird,” was developed by the bird platform (e. charpentier, u. guyet, genomics and bioinformatics core facility genobird, nantes, france) and consists of an analysis pipeline built with snakemake on the same logic as the manual method. a flowchart for data analysis using the bird software is provided in figure s2 in supplementary material., first, raw sequences from fastq files […]

PMCID: 5701242
PMID: 29176637
DOI: 10.1038/s41598-017-16403-4

[…] rna-seq analysis. three samples from each growth condition were depleted for ribosomal rna before reverse transcription., the automated workflow for the rna-seq analysis was implemented in the snakemake programming language, and is available on the supporting website. the workflow includes the following sequential steps: i > read quality control with fastqc […]

PMCID: 5752398
PMID: 29053696
DOI: 10.3791/56129

[…] by the execution of publicly available tools, either from external sources or prepared in-house. the computational pipeline depends on an anaconda-based python 3 virtual environment with the snakemake package available . it runs on machines with unix-like operating system and was tested in a linux environment with the centos 6.5 operating system installed and 40 gb ram […]

PMCID: 4962081
PMID: 27460335
DOI: 10.1038/srep30349

[…] picogreen and equimolar mixed for sequencing using the pgm ion torrent (life technologies)., mothur version 1.34.2 was used to process the 16s rrna partial genes sequences, implemented using a snakemake workflow on a 32-node server running linux ubuntu 14.4. forward and reverse primer sequences were removed from each sample fastq file using flexbar version 2.5. reads were filtered based […]

PMCID: 4344304
PMID: 25723394
DOI: 10.1371/journal.pone.0118438

[…] loaded into two lanes at 5 pm and 10 pm concentrations and subjected to illumina sequencing. demultiplexing was done using illumina casava 1.8.2., the whole analysis pipeline was implemented as a snakemake workflow to keep it reproducible []. sequence matching and counting was done with the mamaslemonpy software that runs under python 3 and is available from the python package index (pypi)., […]

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Snakemake in publications

PMCID: 5902487
PMID: 29692763
DOI: 10.3389/fmicb.2018.00674

[…] 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 […]

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

[…] 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 []., kapac, standing for k-mer activity on polyadenylation site choice, aims to identify k-mers that can explain the change in pas usage observed across samples. for this, […]

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

[…] 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 (). […]

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

[…] as a paired-end 150-cycle run on an illumina hiseq2500 v2 in rapid run mode at the ucsd igm genomics center., 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 […]

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

[…] from 0.94 to 0.99., 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 […]

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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.