Nephele

Nephele leverages cloud computing to process and analyze microbiome and metagenomic sequencing data for taxonomic and functional profiling.

Key Features:

• Cloud-Based Processing: Executes bioinformatics workflows in cloud environments to provide scalable compute for microbiome and metagenomics datasets.
• 16S rRNA Gene Analysis: Processes raw 16S rRNA gene sequencing data using QIIME and mothur for microbial community profiling.
• Whole Genome Shotgun (WGS) Functional Analyses: Analyzes WGS metagenomic data using bioBakery components including MetaPhlAn and HUMMAnN and supports metagenomic assembly with a5-miseq/UDBA-UD for functional and metabolic profiling.
• Dynamic Resource Allocation: Assigns specific tasks within workflows to different types of virtual machines to optimize compute resource utilization.
• Research and Development: Targets improved parallel data processing in cloud environments and addresses resource-allocation inefficiencies identified in Hadoop-based systems.

Scientific Applications:

• Microbial Community Profiling: Profiles microbiome composition and diversity from 16S rRNA gene sequences using QIIME and mothur.
• Taxonomic Profiling of Metagenomes: Generates taxonomic profiles from WGS metagenomic data with MetaPhlAn.
• Functional and Metabolic Profiling: Infers community functional and metabolic capabilities using HUMMAnN and metagenomic assembly outputs.
• Metagenomic Assembly and Downstream Analysis: Performs metagenomic assembly with a5-miseq/UDBA-UD for downstream functional characterization.
• Cloud-Scale Parallel Processing: Enables parallelized processing of large sequencing datasets in cloud environments through task-specific VM allocation.

Methodology:

Uses QIIME and mothur for 16S analysis; employs bioBakery tools including MetaPhlAn and HUMMAnN and metagenomic assembly approaches such as a5-miseq/UDBA-UD; and implements dynamic resource allocation by assigning tasks to various types of virtual machines to improve parallel processing and mitigate Hadoop-related inefficiencies.