Abstract
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.
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Acknowledgments
This publication is supported by an Australian Government Research Training Program (RTP) Scholarship.
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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
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Anderson, R. (2022). Basics of Bash. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 2443. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2067-0_8
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DOI: https://doi.org/10.1007/978-1-0716-2067-0_8
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Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2066-3
Online ISBN: 978-1-0716-2067-0
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