dada2

dada2 infers exact amplicon sequence variants from demultiplexed Illumina-sequenced fastq files to enable accurate, high-resolution characterization of microbial communities.

Key Features:

• Exact Sequence Variant (SV) inference: Infers exact sequence variants that can differ by a single nucleotide rather than clustering reads into Operational Taxonomic Units (OTUs).
• Processing of demultiplexed fastq: Processes demultiplexed fastq files from Illumina-sequenced datasets to derive SVs and sample-wise abundances.
• Error removal: Identifies and removes substitution errors and chimeric sequences to minimize spurious variants.
• Sample-wise abundance output: Outputs precise sequence variants together with their sample-wise abundances.
• Integrated taxonomic classification: Implements the RDP naive Bayesian classifier for taxonomic assignment of sequence variants.
• Benchmarking performance: Demonstrated recovery of a greater number of genuine sequence variants in mock community comparisons.

Scientific Applications:

• Amplicon sequencing analysis: High-resolution characterization of microbial communities from Illumina-sequenced amplicon datasets.
• Mock community benchmarking: Comparative evaluation showing identification of greater numbers of genuine variants in mock communities.
• Intra-species diversity detection: Detection of subtle intra-species variants, exemplified by uncovering diverse Lactobacillus crispatus variants in vaginal samples.
• Taxonomic profiling: Comprehensive microbial community taxonomic classification using the integrated RDP naive Bayesian classifier.

Methodology:

Processes demultiplexed fastq files to infer exact sequence variants, removes substitution and chimera errors, and outputs sequence variants with sample-wise abundances; includes an implementation of the RDP naive Bayesian classifier for taxonomic assignment.