ISEScan

https://github.com/xiezhq/isescan
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ISEScan is a Python pipeline designed to accurately identify and annotate Insertion Sequence (IS)...
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### Install Miniconda3

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Executes the installer script to set up the Miniconda environment.

```bash
sh Miniconda3-latest-Linux-x86_64.sh
```

--------------------------------

### Download Miniconda3 Installer

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Downloads the latest Miniconda3 Linux installer script.

```bash
curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
```

--------------------------------

### Initialize Miniconda3

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Enables conda initialization during the installation process.

```text
Do you wish the installer to initialize Miniconda3
by running conda init? [yes|no]
[no] >>> yes
```

--------------------------------

### Manually Install ISEScan Source

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Extracts the source archive and overwrites existing Python files in the installation directory.

```bash
tar -zxf v1.7.2.2.2.tar.gz
cd ISEScan-1.7.2.2.2/
cp *.py /apps/inst/miniconda3/bin/
```

--------------------------------

### Cleanup and Source Configuration

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Removes the installer script and refreshes the shell environment.

```bash
rm Miniconda3-latest-Linux-x86_64.sh
source ~/.bashrc
```

--------------------------------

### Install ISEScan via Conda

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Installs the ISEScan package from the bioconda channel.

```bash
conda install isescan
```

--------------------------------

### Example genome list file format

Source: https://github.com/xiezhq/isescan/blob/master/README.md

The expected format for the input list file containing paths to FASTA files.

```text
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS014235.scaffolds.fa
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS049959.scaffolds.fa
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS020233.scaffolds.fa
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS022609.scaffolds.fa
/N/dc2/scratch/zhiqxie/hmp/HMASM/SRS024132.scaffolds.fa
```

--------------------------------

### Run ISEScan on a single genome

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Basic commands to execute ISEScan depending on the installation method.

```bash
conda activate base
isescan.py --seqfile NC_012624.fna --output results
```

```bash
python3 /home/xiezhq/projects/ISEScan-1.7.2.2/isescan.py --seqfile genome1.fa --output results
```

--------------------------------

### Verify ISEScan Version

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Checks the currently installed version of ISEScan.

```bash
python3 isescan.py --version
```

```bash
isescan.py --version
```

--------------------------------

### Test ISEScan Execution

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Runs a test analysis on a sequence file to confirm the installation is working correctly.

```bash
python3 isescan.py --seqfile /apps/inst/miniconda3/test/NC_012624.fna --output /home/xiezhq/results --nthread 2
```

--------------------------------

### Locate ISEScan Installation

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Identifies the directory where the ISEScan executable is located.

```bash
which isescan.py
/apps/inst/miniconda3/bin/isescan.py
```

--------------------------------

### Configure SSW library path

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Copy the compiled library and update the library search path.

```bash
cp libssw.so ../
export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH
```

--------------------------------

### Compile SSW library

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Compile the bundled SSW library using gcc.

```bash
cd ssw201507
gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
```

--------------------------------

### Update system PATH for dependencies

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Add the directories containing required bioinformatics tools to the system PATH.

```bash
export PATH=$PATH:/apps/inst/FragGeneScan1.30:/apps/inst/hmmer-3.3/bin:/apps/inst/ncbi-blast-2.10.0+/bin
```

--------------------------------

### Configure Conda Channels

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Adds necessary channels to conda with correct priority settings.

```bash
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```

--------------------------------

### Navigate to ISEScan directory

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Change directory to the extracted ISEScan folder.

```bash
cd ISEScan-1.7.2.2
```

--------------------------------

### Update System PATH

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Adds the ISEScan binary directory to the system PATH if the command is not found.

```bash
export PATH=/apps/inst/miniconda3/bin/:$PATH
```

--------------------------------

### Uncompress ISEScan source files

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Commands to extract the downloaded source archive.

```bash
unzip v1.7.2.2.zip
```

```bash
tar -zvxf v1.7.2.2.tar.gz
```

--------------------------------

### Run ISEScan Analysis

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Executes ISEScan on a sequence file with specified output directory and thread count.

```bash
cp /apps/inst/miniconda3/test/NC_012624.fna ./
isescan.py --seqfile NC_012624.fna --output results --nthread 2
```

--------------------------------

### Configure ISEScan thread usage

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Adjust the number of CPU cores used by ISEScan during execution.

```bash
isescan.py --seqfile genome1.fa --output results --nthread 2
```

--------------------------------

### Upgrade ISEScan via Bioconda

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Updates an existing Bioconda-installed ISEScan instance to the latest available version.

```bash
conda update isescan
```

--------------------------------

### Execute ISEScan in parallel for multiple genomes

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Run multiple ISEScan jobs concurrently using xargs to process a list of genome files.

```bash
nohup cat test.fna.list | xargs -n 1 -P 4 -I{} isescan.py --seqfile {} --output results --nthread 2 > log.txt &
```

--------------------------------

### Retry ISEScan Analysis

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Executes the analysis command after updating the PATH.

```bash
isescan.py --seqfile NC_012624.fna --output results --nthread 2
```

--------------------------------

### Re-run ISEScan

Source: https://github.com/xiezhq/isescan/blob/master/README.md

Command to re-run ISEScan after removing intermediate files to force recalculation.

```bash
isescan.py --seqfile NC_012624.fna --output results
```
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