mothur

mothur processes and analyzes 16S rRNA gene fragment sequencing data to characterize microbial community composition and diversity.

Key Features:

• Comprehensive Workflow: Integrates end-to-end steps for microbial community sequence analysis from raw data processing to downstream diversity analyses.
• Data Processing Capabilities: Performs trimming and screening of sequences to produce high-quality input data.
• Sequence Alignment: Aligns sequences for comparative analyses across samples.
• Distance Calculation: Computes pairwise distances between sequences to inform phylogenetic and clustering analyses.
• Operational Taxonomic Units (OTUs) Assignment: Assigns sequences to OTUs for taxonomic clustering and diversity estimation.
• Diversity Analysis: Calculates alpha and beta diversity metrics to assess within-sample richness/evenness and between-sample differences.

Scientific Applications:

• Microbial ecology (marine ecosystems): Enables detailed characterization of microbial communities from high-throughput 16S rRNA gene sequencing data.

Methodology:

Explicitly performs trimming and screening of sequences, sequence alignment, distance calculation, OTU assignment, and alpha/beta diversity analyses; demonstrated on eight marine samples sequenced by pyrosequencing of 16S rRNA gene fragments with processing of over 222,000 sequences in under two hours on a standard laptop.