Basics of Bash

Use of the Bash command shell and language is one of the fundamental skills of a bioinformatician. This language is required for accessing high performance computing (HPC) services and effectively using these resources to improve your analyses. Bash is completely text based, which is different from...

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Bibliographic Details
Published in:	Methods in molecular biology (Clifton, N.J.) Vol. 2443; p. 161
Main Author:	Anderson, Robyn
Format:	Journal Article
Language:	English
Published:	United States 2022
Subjects:	Computational Biology Computing Methodologies Reproducibility of Results Software Bash fundamentals Linux Command line interface
Online Access:	Get more information
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Summary:	Use of the Bash command shell and language is one of the fundamental skills of a bioinformatician. This language is required for accessing high performance computing (HPC) services and effectively using these resources to improve your analyses. Bash is completely text based, which is different from many graphic based operating systems, but this language is also highly powerful, allowing for significant automation and reproducibility within analysis pipelines. This chapter aims to teach the fundamentals of Bash, including how to create files and folders, how to sort and search through files, and how to use pipes and loops to automate processes. By the end of this chapter, readers should be ready to undertake their first simple bioinformatics analysis.
ISSN:	1940-6029
DOI:	10.1007/978-1-0716-2067-0_8