000K utf8 1100 2020$c2020-11-16 1500 eng 2050 urn:nbn:de:hbz:465-20231214-162457-7 2051 10.1186/s12859-020-03852-4 3000 Welzel, Marius 3010 Beisser, Daniela 3010 Boenigk, Jens 3010 Freisleben, Bernd 3010 Heider, Dominik 3010 Jensen, Manfred 3010 Lange, Anja 3010 Schwarz, Michael 4000 Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads [Welzel, Marius] 4209 Background: Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system. Results: We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub ( https://github.com/MW55/Natrix ) or as a Docker container on DockerHub ( https://hub.docker.com/r/mw55/natrix ). Conclusion: Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data. 4950 https://doi.org/10.1186/s12859-020-03852-4$xR$3Volltext$534 4950 https://nbn-resolving.org/urn:nbn:de:hbz:465-20231214-162457-7$xR$3Volltext$534 4961 https://duepublico2.uni-due.de/receive/duepublico_mods_00077556 5051 570 5550 Amplicon Sequence Variants 5550 Amplicon sequencing 5550 Illumina 5550 Operational Taxonomic Units 5550 Pipline 5550 Snakemake