Extraordinary Command Line: Basic Data Editing Tools for Biologists Dealing with Sequence Data

Q3 Computer Science

Open Bioinformatics Journal Pub Date : 2020-12-31 DOI:10.2174/1875036202013010137

M. Mielczarek, Bartosz Czech, J. Stanczyk, J. Szyda, B. Guldbrandtsen

引用次数: 2

Abstract

The command line is a standard way of using the Linux operating system. It contains many features essential for efficiently handling data editing and analysis processes. Therefore, it is very useful in bioinformatics applications. Commands allow for rapid manipulation of large ASCII files or very numerous files, making basic command line programming skills a critical component in modern life science research. The following article is not a guide to Linux commands. In this manuscript, in contrast to many various Linux manuals, we aim to present basic command line tools helpful in handling biological sequence data. This manuscript provides a collection of simple and popular hacks dedicated to users with very basic experience in the area of the Linux command line. It includes a description of data formats and examples of editing of four types of data formats popular in bioinformatics applications.

查看原文本刊更多论文

非凡的命令行：生物学家处理序列数据的基本数据编辑工具

命令行是使用Linux操作系统的标准方式。它包含许多对有效处理数据编辑和分析过程至关重要的功能。因此，它在生物信息学应用中非常有用。命令允许快速操作大型ASCII文件或大量文件，使基本的命令行编程技能成为现代生命科学研究的关键组成部分。以下文章不是Linux命令的指南。在这份手稿中，与许多不同的Linux手册相比，我们旨在介绍有助于处理生物序列数据的基本命令行工具。这份手稿提供了一组简单而流行的技巧，专门针对在Linux命令行领域有非常基本经验的用户。它包括数据格式的描述，以及在生物信息学应用中流行的四种数据格式的编辑示例。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Open Bioinformatics Journal Computer Science-Computer Science (miscellaneous)

CiteScore

2.40

自引率

0.00%

发文量

期刊介绍： The Open Bioinformatics Journal is an Open Access online journal, which publishes research articles, reviews/mini-reviews, letters, clinical trial studies and guest edited single topic issues in all areas of bioinformatics and computational biology. The coverage includes biomedicine, focusing on large data acquisition, analysis and curation, computational and statistical methods for the modeling and analysis of biological data, and descriptions of new algorithms and databases. The Open Bioinformatics Journal, a peer reviewed journal, is an important and reliable source of current information on the developments in the field. The emphasis will be on publishing quality articles rapidly and freely available worldwide.