AXIOME

AXIOME automates and integrates analysis of small subunit (SSU) rRNA marker data from high-throughput sequencing to support microbial ecology research.

Key Features:

• Integration with QIIME and mothur: Integrates with QIIME and mothur for compatibility with existing microbial ecology workflows.
• Automation of complex analyses: Automates multi-step bioinformatic analyses for processing large high-throughput sequencing datasets.
• Extensibility for customization: Provides extensibility to customize analysis workflows for specific research needs.
• PANDAseq assembly: Implements the PAired-eND Assembler for Illumina sequences (PANDAseq) for paired-end sequence assembly.
• Non-negative matrix factorization (NMF): Utilizes NMF for data reduction and pattern recognition.
• Multi-response permutation procedures (MRPP): Employs MRPP for statistical analysis of community differences.
• SSUnique: Facilitates exploration and recovery of phylogenetic novelty using SSUnique.
• Indicator species analysis: Performs indicator species analysis to identify microbial taxa associated with specific environmental conditions.

Scientific Applications:

• Microbial community profiling: Analyzing microbial community composition and diversity from SSU rRNA marker data generated by high-throughput sequencing.
• Phylogenetic novelty detection: Recovering and exploring novel phylogenetic lineages using SSUnique.
• Pattern discovery: Identifying community structure patterns and reduced-dimension representations via NMF.
• Statistical community comparison: Assessing community-level differences and significance using MRPP.
• Indicator taxa identification: Detecting taxa indicative of specific environmental conditions through indicator species analysis.

Methodology:

Integrates QIIME and mothur; implements PANDAseq for Illumina paired-end assembly; applies non-negative matrix factorization (NMF); performs multi-response permutation procedures (MRPP); employs SSUnique for phylogenetic novelty recovery; and conducts indicator species analysis.