Literature DB >> 33600404

Ten simple rules for getting started with command-line bioinformatics.

Parice A Brandies1, Carolyn J Hogg1.   

Abstract

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Year:  2021        PMID: 33600404      PMCID: PMC7891784          DOI: 10.1371/journal.pcbi.1008645

Source DB:  PubMed          Journal:  PLoS Comput Biol        ISSN: 1553-734X            Impact factor:   4.475


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  24 in total

1.  The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes.

Authors:  Heather Bracken-Grissom; Allen G Collins; Timothy Collins; Keith Crandall; Daniel Distel; Casey Dunn; Gonzalo Giribet; Steven Haddock; Nancy Knowlton; Mark Martindale; Mónica Medina; Charles Messing; Stephen J O'Brien; Gustav Paulay; Nicolas Putnam; Timothy Ravasi; Greg W Rouse; Joseph F Ryan; Anja Schulze; Gert Wörheide; Maja Adamska; Xavier Bailly; Jesse Breinholt; William E Browne; M Christina Diaz; Nathaniel Evans; Jean-François Flot; Nicole Fogarty; Matthew Johnston; Bishoy Kamel; Akito Y Kawahara; Tammy Laberge; Dennis Lavrov; François Michonneau; Leonid L Moroz; Todd Oakley; Karen Osborne; Shirley A Pomponi; Adelaide Rhodes; Scott R Santos; Nori Satoh; Robert W Thacker; Yves Van de Peer; Christian R Voolstra; David Mark Welch; Judith Winston; Xin Zhou
Journal:  J Hered       Date:  2014 Jan-Feb       Impact factor: 2.645

2.  'Big data', Hadoop and cloud computing in genomics.

Authors:  Aisling O'Driscoll; Jurate Daugelaite; Roy D Sleator
Journal:  J Biomed Inform       Date:  2013-07-18       Impact factor: 6.317

3.  Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.

Authors: 
Journal:  J Hered       Date:  2009-11-05       Impact factor: 2.645

4.  Bioconda: sustainable and comprehensive software distribution for the life sciences.

Authors:  Björn Grüning; Ryan Dale; Andreas Sjödin; Brad A Chapman; Jillian Rowe; Christopher H Tomkins-Tinch; Renan Valieris; Johannes Köster
Journal:  Nat Methods       Date:  2018-07       Impact factor: 28.547

5.  The case for cloud computing in genome informatics.

Authors:  Lincoln D Stein
Journal:  Genome Biol       Date:  2010-05-05       Impact factor: 13.583

6.  Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA).

Authors:  Christian R Voolstra; Gert Wörheide; Jose V Lopez
Journal:  Invertebr Syst       Date:  2017-03-16       Impact factor: 2.583

7.  Ten simple rules for biologists learning to program.

Authors:  Maureen A Carey; Jason A Papin
Journal:  PLoS Comput Biol       Date:  2018-01-04       Impact factor: 4.475

8.  Ten simple rules for documenting scientific software.

Authors:  Benjamin D Lee
Journal:  PLoS Comput Biol       Date:  2018-12-20       Impact factor: 4.475

9.  A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference.

Authors:  Adam Cornish; Chittibabu Guda
Journal:  Biomed Res Int       Date:  2015-10-11       Impact factor: 3.411

10.  10KP: A phylodiverse genome sequencing plan.

Authors:  Shifeng Cheng; Michael Melkonian; Stephen A Smith; Samuel Brockington; John M Archibald; Pierre-Marc Delaux; Fay-Wei Li; Barbara Melkonian; Evgeny V Mavrodiev; Wenjing Sun; Yuan Fu; Huanming Yang; Douglas E Soltis; Sean W Graham; Pamela S Soltis; Xin Liu; Xun Xu; Gane Ka-Shu Wong
Journal:  Gigascience       Date:  2018-03-01       Impact factor: 6.524

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  3 in total

1.  FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow.

Authors:  Anna Vlasova; Toni Hermoso Pulido; Francisco Camara; Julia Ponomarenko; Roderic Guigó
Journal:  Genes (Basel)       Date:  2021-10-19       Impact factor: 4.096

2.  Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses.

Authors:  Wendi Bacon; Alexandra Holinski; Marina Pujol; Meredith Wilmott; Sarah L Morgan
Journal:  PLoS Comput Biol       Date:  2022-07-28       Impact factor: 4.779

3.  Improving bioinformatics software quality through incorporation of software engineering practices.

Authors:  Adeeb Noor
Journal:  PeerJ Comput Sci       Date:  2022-01-05
  3 in total

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