Literature DB >> 22908215

Snakemake--a scalable bioinformatics workflow engine.

Johannes Köster1, Sven Rahmann.   

Abstract

SUMMARY: Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. AVAILABILITY: http://snakemake.googlecode.com. CONTACT: johannes.koester@uni-due.de.

Mesh：

Year:  2012        PMID： 22908215     DOI： 10.1093/bioinformatics/bts480

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  664 in total

1.  Fluent genomics with  plyranges and  tximeta.

Authors:  Stuart Lee; Michael Lawrence; Michael I Love
Journal:  F1000Res       Date:  2020-02-12

2.  MutantHuntWGS: A Pipeline for Identifying Saccharomyces cerevisiae Mutations.

Authors:  Mitchell A Ellison; Jennifer L Walker; Patrick J Ropp; Jacob D Durrant; Karen M Arndt
Journal:  G3 (Bethesda)       Date:  2020-09-02       Impact factor: 3.154

3.  ISiCLE: A Quantum Chemistry Pipeline for Establishing in Silico Collision Cross Section Libraries.

Authors:  Sean M Colby; Dennis G Thomas; Jamie R Nuñez; Douglas J Baxter; Kurt R Glaesemann; Joseph M Brown; Meg A Pirrung; Niranjan Govind; Justin G Teeguarden; Thomas O Metz; Ryan S Renslow
Journal:  Anal Chem       Date:  2019-03-06       Impact factor: 6.986

4.  Omics Pipe: a community-based framework for reproducible multi-omics data analysis.

Authors:  Kathleen M Fisch; Tobias Meißner; Louis Gioia; Jean-Christophe Ducom; Tristan M Carland; Salvatore Loguercio; Andrew I Su
Journal:  Bioinformatics       Date:  2015-01-30       Impact factor: 6.937

5.  Bone morphology is regulated modularly by global and regional genetic programs.

Authors:  Shai Eyal; Shiri Kult; Sarah Rubin; Sharon Krief; Neta Felsenthal; Kyriel M Pineault; Dena Leshkowitz; Tomer-Meir Salame; Yoseph Addadi; Deneen M Wellik; Elazar Zelzer
Journal:  Development       Date:  2019-07-26       Impact factor: 6.868

6.  Intra-species differences in population size shape life history and genome evolution.

Authors:  David Willemsen; Rongfeng Cui; Martin Reichard; Dario Riccardo Valenzano
Journal:  Elife       Date:  2020-09-01       Impact factor: 8.140

7.  Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.

Authors:  Michael I Love; Charlotte Soneson; Rob Patro
Journal:  F1000Res       Date:  2018-06-27

8.  The effect of hybridization on transposable element accumulation in an undomesticated fungal species.

Authors:  Mathieu Hénault; Souhir Marsit; Guillaume Charron; Christian R Landry
Journal:  Elife       Date:  2020-09-21       Impact factor: 8.140

9.  Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix.

Authors:  Justin Bedő; Leon Di Stefano; Anthony T Papenfuss
Journal:  Gigascience       Date:  2020-11-18       Impact factor: 6.524

10.  The Role of Omega-3 Polyunsaturated Fatty Acids from Different Sources in Bone Development.

Authors:  Reut Rozner; Janna Vernikov; Shelley Griess-Fishheimer; Tamar Travinsky; Svetlana Penn; Betty Schwartz; Ronit Mesilati-Stahy; Nurit Argov-Argaman; Ron Shahar; Efrat Monsonego-Ornan
Journal:  Nutrients       Date:  2020-11-13       Impact factor: 5.717
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