ASaiM

ASaiM provides integrated analysis of microbiota sequencing data within the Galaxy platform, enabling processing of raw metataxonomic, metagenomic, and metatranscriptomic reads into taxonomic and functional characterizations.

Key Features:

• Comprehensive analytical toolset: Tools for assembling reads, extracting features, exploring microbial composition, and visualizing results from raw metataxonomic, metagenomic, and metatranscriptomic sequences.
• Customizable workflows: Galaxy-based customizable workflows for stepwise execution of metagenomic and metatranscriptomic analyses.
• Scalability: Deployable as a Galaxy Docker flavor and capable of running on standard computers or high-performance computing clusters to process large numbers of datasets.
• Reproducibility and shareability: Integration within the Galaxy framework to enable transparent, reproducible, and shareable analyses.

Scientific Applications:

• Metagenomics: Analysis of genetic material recovered directly from environmental samples to study microbial diversity and function.
• Metatranscriptomics: Investigation of RNA transcripts to profile gene expression patterns within microbial communities.
• Microbiota studies: Characterization of microbiota composition and dynamics in environments including human health and disease contexts.

Methodology:

Integration of Galaxy-compatible bioinformatics tools with computational steps including assembly of sequencing reads into contigs or transcripts, feature extraction (genes, pathways, taxa), statistical exploratory analyses, and generation of visualizations.