Cleanifier

Cleanifier removes human contamination from microbial sequences using spaced seeds of a human pangenome index.

Key Features:

• Alignment-free detection: Detects human contamination based on gapped k-mers, or spaced seeds, without sequence alignment.
• Pangenome index: Uses a pangenome index of known human gapped k-mers, with support for creating and using alternative references.
• Dual filtering modes: Supports querying all gapped k-mers or only a sampled subset of them.
• Probabilistic indexing: Offers exact and probabilistic k-mer indexing options, including a probabilistic Cuckoo filter to store the complete k-mer set.
• Flexible sampling: Can use different sampling methods on the same index.

Scientific Applications:

• Human-derived microbiome data processing: Removes human sequences to comply with privacy and data protection guidelines for human sequence data.
• Downstream metagenomic analysis: Prevents human contamination from causing problems in metagenomic binning or genome assembly.
• Large-scale metagenomics: Enables fast and accurate contamination removal for large-scale metagenomics projects.

Methodology:

Reads are classified and filtered according to their gapped k-mer content against a pangenome index of known human gapped k-mers.