Orione

Orione provides integrative analysis of next-generation sequencing (NGS) microbial data, supporting quality check, alignment, assembly, scaffolding, and annotation to enable reproducible end-to-end microbiology research.

Key Features:

• Galaxy platform: Built on the Galaxy platform and integrates publicly available research software to support workflow construction.
• Pipelines: Provides specifically designed pipelines for NGS microbiology data analysis and reproducible workflow execution.
• Quality check: Performs quality assessment of NGS reads for microbial datasets.
• Alignment: Supports read alignment for applications such as bacterial resequencing and bacterial RNA-Seq.
• De novo assembly: Supports de novo assembly of microbial genomes.
• Scaffolding: Performs scaffolding to order and orient contigs during genome reconstruction.
• Gene annotation: Supports gene annotation for assembled microbial genomes.
• Bacterial RNA-Seq: Supports workflows for bacterial transcriptomic analysis.
• Bacterial resequencing: Supports resequencing analyses for bacterial comparative genomics.
• Metagenomics: Supports metagenomic analyses of microbial communities.
• Reproducibility and interoperability: Provides a transparent framework to enhance reproducibility and interoperability of computational analyses.

Scientific Applications:

• Bacterial resequencing: Comparative analysis of bacterial genomes using resequencing workflows.
• De novo assembly and scaffolding: Reconstruction of microbial genomes from NGS reads through assembly and scaffolding.
• Bacterial RNA-Seq: Transcriptome profiling of bacteria using RNA-Seq workflows.
• Gene annotation: Functional annotation of genes in assembled microbial genomes.
• Metagenomics: Analysis of microbial community composition and function from metagenomic data.
• End-to-end NGS microbiology research: Integrated processing from raw reads to annotated assemblies to support complete microbiology research projects.

Methodology:

Computational steps explicitly include quality check, alignment, assembly, scaffolding, and annotation executed via integrated pipelines using publicly available research software on the Galaxy platform.