MerCat2

MerCat2 performs k-mer counting and feature extraction on omics sequences by processing massively parallel sequencing raw reads, assembled contigs, and protein sequences (for any specified length k) to produce feature abundance counts tables, quality-control reports, protein feature metrics, and PCA visualizations for database-independent analysis.

Key Features:

• Parallel, scalable processing: Executes parallel and scalable computation to handle large omics datasets.
• Versatile k-mer counting: Counts k-mers of any specified length k across nucleotide and protein inputs.
• Input types: Accepts massively parallel sequencing raw reads, assembled contigs, and protein sequences from any platform.
• Output generation: Produces feature abundance counts tables, quality-control reports, and protein feature metrics.
• Visualization: Provides graphical representations such as principal component analysis (PCA).
• Database-independent analysis: Initializes all data for direct property analysis without dependence on external reference databases.
• Cross-examination capabilities: Enables rapid cross-examination and comparison of omics data within a sample.

Scientific Applications:

• K-mer-based profiling: Generating k-mer-derived feature profiles from sequencing reads, contigs, and proteins.
• Assembly- and database-independent property analysis: Directly analyzing sequence-derived properties without reference databases.
• Quality assessment: Producing quality-control reports for sequencing reads and assemblies.
• Protein feature analysis: Deriving protein feature metrics from protein sequence input.
• Within-sample comparative analysis: Facilitating rapid cross-examination and comparison of omics data within a sample.

Methodology:

Performs parallel, scalable k-mer counting for any specified k on input raw reads, assembled contigs, and protein sequences; generates feature abundance counts tables, quality-control reports, protein feature metrics, and PCA visualizations using a database-independent initialization of all data for direct property analysis.