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

ABSTRACT:

Motivation

The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.

Results

We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers

SUBMITTER: Zentgraf J 

PROVIDER: S-EPMC12758600 | biostudies-literature | 2026 Jan

REPOSITORIES: biostudies-literature