CANGS

CANGS processes amplicon-based 454 GS-FLX sequencing data to perform preprocessing and taxonomic assignment for biodiversity surveys.

Key Features:

• Quality Control and Trimming: Filters low-quality sequences and trims reads to retain high-confidence data for downstream analyses.
• PCR Primer Removal: Removes PCR primer sequences from reads to prevent primer-derived artifacts.
• Singleton Filtering: Filters out singleton sequences (those appearing only once) to reduce the impact of potential sequencing errors.
• Barcode Identification: Identifies sample barcodes within reads to enable differentiation of multiplexed samples.
• File Generation for Downstream Analysis: Generates input files compatible with third-party tools for analyses such as rarefaction and with custom scripts.
• Taxonomic Assignment: Assigns taxonomic names by comparing sequences against reference sequences in the NCBI database.
• Adaptability: Handles various amplicon sizes, primer sequences, and quality threshold settings for different sequencing projects.

Scientific Applications:

• Amplicon-based biodiversity surveys: Preprocesses and prepares 454 GS-FLX amplicon data for biodiversity assessment.
• Taxonomic analysis: Assigns sequences to taxonomic groups via similarity searches against NCBI reference sequences.
• Multiplexed sample processing: Enables differentiation and tracking of multiplexed samples using barcode identification.
• Diversity and rarefaction analyses: Produces files suitable for rarefaction and other diversity analyses.

Methodology:

Performs quality filtering and trimming, removes PCR primers, filters singletons, identifies barcodes, generates files for downstream analyses (including rarefaction), and assigns taxonomy by comparing sequences to NCBI reference sequences; implemented in Perl and runs on Mac OS X/Linux.