CDSnake

CDSnake implements a Snakemake pipeline to retrieve annotated Operational Taxonomic Units (OTUs) from Illumina paired-end 16S rRNA gene reads using CD-HIT-OTU-MiSeq utilities.

Key Features:

• Avoidance of Read Merging: Clusters paired reads separately using CD-HIT-OTU-MiSeq to avoid merging overlapping 3' end regions of Illumina reads.
• Snakemake Integration: Orchestrates CD-HIT-OTU-MiSeq steps within a Snakemake workflow to automate execution and ensure reproducible runs.
• Scalability and Automation: Automates CD-HIT-OTU-MiSeq execution to enable processing of large metagenomic 16S datasets.
• Benchmarking Performance: In comparisons with QIIME2-DADA2 and deblur on mock Balanced and HMP datasets, produced OTU counts closer to the actual number of strains and retained higher total read counts while generally running slower.
• Enhanced Data Preservation: Preserves higher total counts from raw data by leveraging CD-HIT-OTU-MiSeq clustering properties.

Scientific Applications:

• OTU retrieval from paired-end 16S data: Retrieval and annotation of OTUs from Illumina paired-end 16S rRNA gene metagenomic datasets.
• Benchmarking and method comparison: Comparative evaluation of OTU-calling performance against QIIME2-DADA2 and deblur using mock community datasets (Balanced and HMP).
• Microbial community profiling: Analyses of microbial community composition where preserving raw counts and accurate OTU numbers is important for downstream ecological interpretation.

Methodology:

Implements CD-HIT-OTU-MiSeq utilities to cluster paired-end Illumina reads without merging, orchestrated via a Snakemake workflow.