Abstract
BackgroundLong-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. As a result, long-read sequencing platforms are becoming more popular. In this respect, the Oxford Nanopore Technologies–based long-read sequencing “nanopore" platform is becoming a widely used tool with a broad range of applications and end-users. However, the need to explore and manipulate the complex data generated by long-read sequencing platforms necessitates accompanying specialized bioinformatics platforms and tools to process the long-read data correctly. Importantly, such tools should additionally help democratize bioinformatics analysis by enabling easy access and ease-of-use solutions for researchers.ResultsThe Galaxy platform provides a user-friendly interface to computational command line–based tools, handles the software dependencies, and provides refined workflows. The users do not have to possess programming experience or extended computer skills. The interface enables researchers to perform powerful bioinformatics analysis, including the assembly and analysis of short- or long-read sequence data. The newly developed “NanoGalaxy" is a Galaxy-based toolkit for analysing long-read sequencing data, which is suitable for diverse applications, including de novo genome assembly from genomic, metagenomic, and plasmid sequence reads.ConclusionsA range of best-practice tools and workflows for long-read sequence genome assembly has been integrated into a NanoGalaxy platform to facilitate easy access and use of bioinformatics tools for researchers. NanoGalaxy is freely available at the European Galaxy server https://nanopore.usegalaxy.eu with supporting self-learning training material available at https://training.galaxyproject.org.
Highlights
Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation
We have integrated a large collection of long-read sequence tools into the Galaxy platform, the NanoGalaxy toolkit, including diverse applications for the analyses of long-read sequences (Table 1)
To increase the utility of this toolkit, we have developed a set of Galaxy workflows performing common analysis tasks using the tools in the NanoGalaxy toolkit
Summary
Long-read sequencing can be applied to generate very long contigs and even completely assembled genomes at relatively low cost and with minimal sample preparation. The 2 prominent long-read sequencing platforms are nanopore sequencing by Oxford Nanopore Technologies and single-molecule real-time sequencing by Pacific Biosciences [5,6] These platforms generate sequence reads much longer than those of the classic short-read technologies, including long reads from single DNA molecules and without the need of PCR amplification (>10 kb on average). Utilizing these technologies, library preparation and sequencing may be performed outside of traditional research laboratories, with sequencing outputs generated in real time [7]. The (rapid) detection of AMR pathogens and their resistances in diseases, food, and the environment are pillars by which increasing AMR could be detected, monitored, and prevented
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
