Snakemake - a scalable bioinformatics workflow engine

By Johannes Köster, Sven Rahmann. Bioinform., 2018

1,786 citations recorded by the source corpus.

Subfields: Information Systems and Management, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/625bdb87e5750faf96fd0c59cb274ff9dda9cbb3

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Information Systems and Management

1. Trevor Bedford
2. K. Kistler

In Molecular Biology

1. Michael D. Lee
2. A. M. Eren
3. Tom O. Delmont
4. Trevor Bedford
5. S. Geisen
6. K. Kistler

Citations in the corpus

• ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation (2020, neutral): “∗ , for > 0 (6) "̅ = ∑ * + - for < 0 (7) The default ranges for the widths are $ = [10,30] and $" = [20,50].”
• Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229e (2020, positive): “A Snakemake file ( Ko¨ster and Rahmann, 2012 ) within each HCoV directory follows the general outline of a Nextstrain build (Nextstrain, RRID:SCR_018223) and was used to align each gene to a reference strain and build a time-resolved phylogeny with IQ-Tree v1 ( Nguyen et al., 2015 ) and TimeTree (…”
• Community-led, integrated, reproducible multi-omics with anvi’o (2020, methodology): “The anvi’o workflows are powered by Snakemake 15 , which ensures relatively easy deployment to any computer system and automatic parallelisation of independent analysis steps.”
• Sustainable data analysis with Snakemake (2021, neutral): “Third, with systems like Nextflow [29], Snakemake [18], BioQueue [33], Bpipe [26], ClusterFlow [11], Cylc [25], and BigDataScript [8], workflows are specified using a domain specific language (DSL).”
• VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses (2021, neutral): “S8), but VirSorter2 ’ s internal processes are highly parallelizable, and written with snakemake, a cutting-edge pipeline management tool designed for computer clusters [58].”
• Integrating quantitative morphological and qualitative molecular methods to analyse soil nematode community responses to plant range expansion (2018, methodology): “Snakemake—a scalable bioinformatics workflow engine.”