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ASCIIGenome: a command line genome browser for console terminals
SUMMARY: Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2017
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423454/ https://www.ncbi.nlm.nih.gov/pubmed/28119307 http://dx.doi.org/10.1093/bioinformatics/btx007 |
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author | Beraldi, Dario |
author_facet | Beraldi, Dario |
author_sort | Beraldi, Dario |
collection | PubMed |
description | SUMMARY: Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. IMPLEMENTATION: ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. AVAILABILITY AND IMPLEMENTATION: Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5423454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-54234542017-05-11 ASCIIGenome: a command line genome browser for console terminals Beraldi, Dario Bioinformatics Applications Notes SUMMARY: Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. IMPLEMENTATION: ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. AVAILABILITY AND IMPLEMENTATION: Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-05-15 2017-01-24 /pmc/articles/PMC5423454/ /pubmed/28119307 http://dx.doi.org/10.1093/bioinformatics/btx007 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Beraldi, Dario ASCIIGenome: a command line genome browser for console terminals |
title | ASCIIGenome: a command line genome browser for console terminals |
title_full | ASCIIGenome: a command line genome browser for console terminals |
title_fullStr | ASCIIGenome: a command line genome browser for console terminals |
title_full_unstemmed | ASCIIGenome: a command line genome browser for console terminals |
title_short | ASCIIGenome: a command line genome browser for console terminals |
title_sort | asciigenome: a command line genome browser for console terminals |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423454/ https://www.ncbi.nlm.nih.gov/pubmed/28119307 http://dx.doi.org/10.1093/bioinformatics/btx007 |
work_keys_str_mv | AT beraldidario asciigenomeacommandlinegenomebrowserforconsoleterminals |