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Ten recommendations for creating usable bioinformatics command line software

Torsten Seemann

Author Affiliations

Victorian Bioinformatics Consortium, Building 76 Monash University Clayton, Clayton, VIC 3800, Australia

Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, 187 Grattan St, Carlton, Melbourne, VIC 3010, Australia

GigaScience 2013, 2:15  doi:10.1186/2047-217X-2-15

Published: 13 November 2013


Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Bioinformatics software; Software quality; User interface; Unix; Tools