Cascabel

Cascabel processes amplicon sequence data to analyze marker gene sequencing targets such as the rRNA operon (16S, 18S, ITS) and cytochrome c oxidase I (CO1) for assessment of microbial and environmental DNA (eDNA) communities.

Key Features:

• Workflow engine: Implemented with Snakemake for workflow management.
• Input data: Accepts raw sequence data as input.
• Outputs: Produces an operational taxonomic unit (OTU) table and a representative sequence tree.
• OTU generation: Provides multiple selectable OTU generating methods.
• Methods integration: Integrates existing solutions and newly developed computational methods.
• Scalability: Supports execution across computing environments from personal computers to high-performance computing servers.

Scientific Applications:

• Marker gene sequencing: Analysis of single-gene marker sequences (16S, 18S, ITS, CO1) for taxonomic profiling.
• Microbial community assessment: Characterization of microbial communities in diverse environmental samples.
• eDNA surveys: Environmental DNA sequencing analyses targeting multicellular organisms.
• Plant and animal microbiomes: Investigation of microbiomes associated with plants and animals.
• Cost-effective diversity surveys: Single-gene sequencing alternative to whole-genome approaches for biodiversity assessment.

Methodology:

Implemented as a Snakemake workflow that accepts raw sequence data, integrates existing and newly developed computational methods, supports multiple OTU generating methods, and outputs an OTU table and a representative sequence tree.