Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.

ABSTRACT:

Background

The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.

Methods

This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as t

SUBMITTER: Orschanski D 

PROVIDER: S-EPMC12613601 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature