Targeted decontamination of sequencing data with CLEAN.

ABSTRACT: Many biological and medical questions are answered based on the analysis of sequence data. However, we can find contamination, artificial spike-ins, and overrepresented rRNA (ribosomal RNA) sequences in various read collections and assemblies. In particular, spike-ins used as controls, as those known from Illumina or Nanopore data, are often not considered as contaminants and also not appropriately removed during analyses. Additionally, removing human host DNA may be necessary for data protection and ethical considerations to ensure that individuals cannot be identified. We developed CLEAN, a pipeline to remove unwanted sequences from both long- and short-read sequencing techniques. While focusing on Illumina and Nanopore data with their technology-specific control sequences, the pipeline

SUBMITTER: Lataretu M 

PROVIDER: S-EPMC12288876 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature