Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

ABSTRACT:

Background

Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively.

Results

Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent

SUBMITTER: Rosenboom I 

PROVIDER: S-EPMC9650795 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature