# dix-seq

**Repository Path**: dpsh/dix-seq

## Basic Information

- **Project Name**: dix-seq
- **Description**: Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples, and exports statistical and visual results automatically with only one step!
- **Primary Language**: Perl
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 0
- **Created**: 2022-08-09
- **Last Updated**: 2025-07-15

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

## Dix-seq: An integrated pipeline for fast amplicon data analysis
<hr>

### 1. Abstract

The amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing. Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers. 

### 2. Dependencies and Install

INSTALL.md

### 3. Get to start

#### 3.1 install dix-seq

##### 3.1.1 Build from Source

```sh
git clone https://gitee.com/dpsh/dix-seq
```

##### 3.1.2 Installation by [singularity or Apptainer](https://github.com/apptainer/singularity) image `dix-seq.sif` from [figshare](https://figshare.com/ndownloader/files/40986824)

```sh
wget https://figshare.com/ndownloader/files/40986824
mv 40986824 dix-seq.sif
```

#### 3.2 install USEARCH

```sh
wget https://github.com/rcedgar/usearch_old_binaries/blob/main/bin/usearch11.0.667_i86linux64
mv usearch11.0.667_i86linux64 usearch
chmod -R 775 usearch
mv  usearch dix-seq/binaries
```

`Recommend:` use other USEARCH 64bit version: https://github.com/rcedgar/usearch_old_binaries

#### 3.3 install USEARCH SINTAX db

```sh
cd dix-seq/db
wget -O PR2_4.14.zip https://zenodo.org/record/6976950/files/PR2_4.14.zip?download=1
wget -O rdp_16s_v18_sp.zip https://zenodo.org/record/6976950/files/rdp_16s_v18_sp.zip?download=1
wget -O unite_10.05.2021.zip https://zenodo.org/record/6976950/files/unite_10.05.2021.zip?download=1
unzip PR2_4.14.zip
unzip rdp_16s_v18_sp.zip
unzip unite_10.05.2021.zip
../binaries/usearch -makeudb_usearch  rdp_16s_v18_sp.fasta  -output  rdp_16s_v18_sp.udb
../binaries/usearch -makeudb_usearch  PR2_4.14.fasta  -output  PR2_4.14.udb
../binaries/usearch -makeudb_usearch  unite_10.05.2021.fasta  -output  unite_10.05.2021.udb
```

#### 3.4 run example in Linux system

##### 3.4.1 run example directly in command line
Go to example dir and get the template file

```sh
dix-seq metadata.txt validate
dix-seq metadata.txt pipeline
```

##### 3.4.2 run example in virtual machine sandbox (Windows WLS2 also supported)
run the example in sandbox by using singularity with `dix-seq.sif` from [figshare](https://figshare.com/ndownloader/files/40986824)



```sh
singularity exec -B $PWD,/devel/apptainer/db dix-seq.sif dix-seq metadata.txt pipeline,function_wf,advanced,summarize,report
```
**Notice:** `-B` is set for binding directory, using `,` to set multiple paths; `/devel/apptainer/db` was the real path (Out of the sandbox), and that path should be same in the `metadata.txt` of `db`.



### 4. citation
   
```text 
Dix-seq: An integrated pipeline for fast amplicon data analysis
https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100120

DOI：10.59717/j.xinn-life.2024.100120

Dong P., Chen Y., Wei Y., et al. (2025). Dix-seq: An integrated pipeline for fast amplicon data analysis. The Innovation Life 3: 100120.
```