Kontaminant

Kontaminant performs k-mer-based screening and host-sequence subtraction to reduce contaminant reads and enrich putative viral nucleic acids from next-generation sequencing (NGS) data derived from eukaryotic tissue samples.

Key Features:

• K-mer-Based Filtering: Employs a k-mer frequency-based filter to reduce the number of contigs prior to assembly and focus on putative viral nucleic acids.
• Pre-Assembly Host-Mapping Subtraction: Integrates short-read mapping tools to subtract host sequences before assembly.
• Low Complexity Filter: Removes low-complexity, non-informative reads to refine input datasets for assembly.

Scientific Applications:

• Viral discovery from eukaryotic tissues: Enables identification of novel viral sequences in complex eukaryotic tissue NGS datasets.
• Contig reduction and assembly improvement: Reduces the number of assembled contigs (reported up to 99.97%) and increases viral contig size to simplify downstream analysis.
• Validation and benchmarking: Has been validated on Illumina sequencing of naturally infected liver tissue and on simulated datasets.

Methodology:

Applies k-mer frequency-based filtering, low-complexity read filtering, and short-read mapping-based host subtraction prior to assembly.