Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads

Abstract

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.

NOREC4DNA: using near-optimal rateless erasure codes for DNA storage

“…Since NOREC4DNA reads FASTA files line by line, sorting the clustered sequences by how often the sequences have been sequenced will allow NOREC4DNA to work more reliably. While most modern sequencing pipelines perform these steps accordingly, we use the Snakemake-based pipeline ‘Natrix’ [ 33 ].…”

Quantification of the covariation of lake microbiomes and environmental variables using a machine learning‐based framework

“…Adapter removal, quality trimming, and demultiplexing using index sequences were performed by the sequencing company (Fasteris). Sequence processing was performed using a provisional version of the Natrix pipeline (Welzel et al, 2020). Base quality of raw sequence reads was rechecked using the fastqc software (v0.11.5; Andrews, 2010) and reads with an average Phred quality score below 25 or with at least one base with a Phred quality score below 15 were removed using prinseq‐lite (v0.20.4; Schmieder & Edwards, 2011).…”

A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes

“…For the amplicon analysis, we used the standardized workflow Natrix, including (i) quality filtering, (ii) clustering, and (iii) taxonomy annotation ( Welzel et al, 2020 ). The quality of the sequencing reads was re-checked using FastQC (v0.11.8), and low-quality tails were removed from the reads using PRINSEQ ( Schmieder and Edwards, 2011 ) (v0.20.4).…”