easyfm : An easy software suite for file manipulation of Next Generation Sequencing data on desktops

Abstract

Storing and manipulating Next Generation Sequencing (NGS) file formats is an essential but difficult task in biological data analysis. The easyfm (easy file manipulation) toolkit (https://github.com/TaekAndBrendan/easyfm) makes manipulating commonly used NGS files more accessible to biologists. It enables them to perform end-to-end reproducible data analyses using a free standalone desktop application (available on Windows, Mac and Linux). Unlike existing tools (e.g. Galaxy), the Graphical User Interface (GUI)-based easyfm is not dependent on any high-performance computing (HPC) system and can be operated without an internet connection. This specific benefit allow easyfm to seamlessly integrate visual and interactive representations of NGS files, supporting a wider scope of bioinformatics applications in the life sciences. Author summaryThe analysis and manipulation of NGS data for understanding biological phenomena is an increasingly important aspect in the life sciences. Yet, most methods for analysing, storing and manipulating NGS data require complex command-line tools in HPC or web-based servers and have not yet been implemented in comprehensive, easy-to-use software. This is a major hurdle preventing more general application in the field of NGS data analysis and file manipulation. Here we present easyfm, a free standalone Graphical User Interface (GUI) software with Python support that can be used to facilitate the rapid discovery of target sequences (or users interest) in NGS datasets for novice users. For user-friendliness and convenience, easyfm was developed with four work modules and a secondary GUI window (herein secondary window), covering different aspects of NGS data analysis (mainly focusing on FASTA files), including post-processing, filtering, format conversion, generating results, real-time log, and help. In combination with the executable tools (BLAST+ and BLAT) and Python, easyfm allows the user to set analysis parameters, select/extract regions of interest, examine the input and output results, and convert to a wide range of file formats. To help augment the functionality of existing web-based and command-line tools, easyfm, a self-contained program, comes with extensive documentation (hosted at https://github.com/TaekAndBrendan/easyfm) including a comprehensive step-by-step guide.