Distanced

Distanced estimates microbial sequence diversity by correcting mean pairwise distances for sequencing errors using a Bayesian approach to produce accurate alpha diversity measures from rDNA and other sequences.

Key Features:

• Error correction: Corrects for sequencing errors that inflate observed sequence diversity to provide more accurate diversity estimates.
• Bayesian approach: Uses a Bayesian statistical framework to infer sequence differences in the absence of sequencing errors and adjust mean pairwise distance.
• Mean pairwise distance metric: Focuses on mean pairwise distance as the measure of within-sample (alpha) diversity.
• Versatility across sequence types: Applicable to microbial rDNA sequences and non-microbial sequences such as antibody mRNA.
• Performance evaluation: Demonstrates lower root mean square prediction error (RMSPE) compared to DADA2 and Deblur in reported comparisons.
• Optional reference sequences (FASTA): Accepts an optional set of reference sequences in FASTA format for additional accuracy checks.
• Input format (FASTQ): Operates on DNA sequence reads provided in FASTQ format.

Scientific Applications:

• Alpha diversity estimation: Produces corrected alpha diversity measures of microbial communities by adjusting mean pairwise distance for sequencing errors.
• Microbial rDNA analysis: Applied to rDNA sequences from bacteria, fungi, and other organisms to assess within-sample diversity.
• Immunogenomics / antibody analysis: Applicable to antibody mRNA sequence data for diversity estimation.
• Ecology and environmental science: Supports studies of microbial community diversity in ecological and environmental research.
• Human health-related microbiome research: Supports analyses where accurate microbial diversity impacts human health studies.

Methodology:

Applies a Bayesian statistical approach to correct the mean pairwise distance (within-sample diversity) for expected increases due to sequencing errors.