Dix-seq: An integrated pipeline for fast amplicon data analysis

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Update: version 1.0.0

Notes: USEARCH (https://github.com/rcedgar/usearch12) was open sourced and donated to the public domain, So we integrated USEARCH (usearch11.0.667_i86linux64) into prebuilt APPTAINER sif image.

1. abstract

Rapid advancements in sequencing technologies in the past decade have driven the widespread adoption of amplicon analysis. Various software has been developed for amplicon data analysis. However, current software/pipelines often require manual intervention between multiple steps, necessitating a clear understanding of parameters and hindering inexperienced users from automating their workflows. Here, we introduce an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing. Dix-seq integrated more than 21 algorithms, software, and third-party procedures into eight modules, enabling the analysis from raw amplicon sequences to various statistical and visualization results. The pipeline achieves highlevels of automation through the use of a parameter card file, which consolidates all settings and allows users to complete the entire data analysis with a single command in one step. Furthermore, Dix-seq’s modular design and scalability enable experienced users to fine-tune the workflow to their needs, ensuring reproducible and customizable analysis. Benchmarks performed on datasets from two real-world case studies demonstrated that Dix-seq excels in extracting biologically meaningful patterns, generating publish-ready figures integrated with statistical information, and retaining/detecting variance even at low sequencing depths. In summary, Dix-seq is a fast, convenient, and versatile tool for amplicon analysis. It is tailored towards both entry-level and experienced users, providing publication-ready results with a single command while maintaining customizability and reproducibility.

2. build images

apptainer build --fakeroot dix-seq-1.0.0.sif  dix-seq-1.0.0.def

3. INSTALL and get start

Get prebuilt dix-seq sif file and db files from figshare.

#download sif image
wget https://figshare.com/ndownloader/files/51022509 -O dix-seq-1.0.0.sif

#download db file
wget  https://figshare.com/ndownloader/files/51060284  -O db.tar.gz
tar xzvf db.tar.gz

#download test data
wget https://figshare.com/ndownloader/files/51047609 -O test-data.tar.gz
tar xzvf test-data.tar.gz; mv test-data/* ./; rm -rf test-data

#modify metadata.txt file, setting project_home,project_id,raw_data,mapping_file and db location.

#validate metadata and fastq files.
apptainer exec dix-seq-1.0.0.sif dix-seq metadata.txt validate

#use pipeline for standand analysis.
apptainer exec dix-seq-1.0.0.sif dix-seq metadata.txt pipeline

4. misc

Step By Step Data Analysis For Amplicon Sequencing Data

Dix-seq: 扩增子数据分析工作流使用说明