CCMetagen

CCMetagen classifies organisms in metagenomes and metatranscriptomes by weighing all high-scoring read mappings against the entire reference database to improve taxonomic assignment accuracy for analyses of high-throughput sequencing data.

Key Features:

• Advanced Read Mapping: Weighs all high-scoring read mappings collectively against the entire reference database to produce more informed alignments.
• High Precision and F1 Scores: Demonstrated superior species-level precision (3–1580-fold increases) and F1 scores (2–922-fold increases) relative to Kraken2, Centrifuge, and KrakenUniq in simulated fungal and bacterial metagenomes.
• Comprehensive Reference Database: Supports using the entire NCBI nucleotide collection (nt) as reference, enabling assessment of species with incomplete genome sequences across all biological kingdoms.
• Efficiency: Operates with fast runtime and memory-efficient requirements suitable for large-scale analyses.

Scientific Applications:

• Microbiome species-level profiling: Provides accurate species-level classification in microbiome studies.
• Eukaryotic and prokaryotic community analysis: Processes complex datasets containing both eukaryotic and prokaryotic organisms.
• Environmental and host-associated microbial community studies: Supports analysis of environmental and host-associated microbial communities from metagenomic and metatranscriptomic data.

Methodology:

Collectively weighs high-scoring read mappings against the reference database and supports use of the NCBI nucleotide collection (nt) as the reference.