Literature DB >> 31477884

Workflow systems turn raw data into scientific knowledge.

Jeffrey M Perkel.   

Abstract

Keywords:  Computational biology and bioinformatics; Genomics; Software

Mesh：

Year:  2019        PMID： 31477884     DOI： 10.1038/d41586-019-02619-z

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   49.962


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  16 in total

1.  Challenge to scientists: does your ten-year-old code still run?

Authors:  Jeffrey M Perkel
Journal:  Nature       Date:  2020-08       Impact factor: 49.962

2.  poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

Authors:  Christian Brandt; Sebastian Krautwurst; Riccardo Spott; Mara Lohde; Mateusz Jundzill; Mike Marquet; Martin Hölzer
Journal:  Front Genet       Date:  2021-07-28       Impact factor: 4.599

Review 3.  A simple guide to de novo transcriptome assembly and annotation.

Authors:  Venket Raghavan; Louis Kraft; Fantin Mesny; Linda Rigerte
Journal:  Brief Bioinform       Date:  2022-03-10       Impact factor: 11.622

4.  miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

Authors:  Fabian Kern; Tobias Fehlmann; Jeffrey Solomon; Louisa Schwed; Nadja Grammes; Christina Backes; Kendall Van Keuren-Jensen; David Wesley Craig; Eckart Meese; Andreas Keller
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

5.  Recovering prokaryotic genomes from host-associated, short-read shotgun metagenomic sequencing data.

Authors:  Sara Saheb Kashaf; Alexandre Almeida; Julia A Segre; Robert D Finn
Journal:  Nat Protoc       Date:  2021-04-16       Impact factor: 13.491

6.  PM4NGS, a project management framework for next-generation sequencing data analysis.

Authors:  Roberto Vera Alvarez; Lorinc Pongor; Leonardo Mariño-Ramírez; David Landsman
Journal:  Gigascience       Date:  2021-01-07       Impact factor: 6.524

7.  Ten simple rules to cultivate transdisciplinary collaboration in data science.

Authors:  Faryad Sahneh; Meghan A Balk; Marina Kisley; Chi-Kwan Chan; Mercury Fox; Brian Nord; Eric Lyons; Tyson Swetnam; Daniela Huppenkothen; Will Sutherland; Ramona L Walls; Daven P Quinn; Tonantzin Tarin; David LeBauer; David Ribes; Dunbar P Birnie; Carol Lushbough; Eric Carr; Grey Nearing; Jeremy Fischer; Kevin Tyle; Luis Carrasco; Meagan Lang; Peter W Rose; Richard R Rushforth; Samapriya Roy; Thomas Matheson; Tina Lee; C Titus Brown; Tracy K Teal; Monica Papeș; Stephen Kobourov; Nirav Merchant
Journal:  PLoS Comput Biol       Date:  2021-05-13       Impact factor: 4.475

Review 8.  Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap.

Authors: 
Journal:  BMJ Glob Health       Date:  2020-11

9.  An open-source, end-to-end workflow for multidimensional photoemission spectroscopy.

Authors:  R Patrick Xian; Yves Acremann; Steinn Y Agustsson; Maciej Dendzik; Kevin Bühlmann; Davide Curcio; Dmytro Kutnyakhov; Federico Pressacco; Michael Heber; Shuo Dong; Tommaso Pincelli; Jure Demsar; Wilfried Wurth; Philip Hofmann; Martin Wolf; Markus Scheidgen; Laurenz Rettig; Ralph Ernstorfer
Journal:  Sci Data       Date:  2020-12-17       Impact factor: 6.444

10.  RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow.

Authors:  Marie Lataretu; Martin Hölzer
Journal:  Genes (Basel)       Date:  2020-12-10       Impact factor: 4.096
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