### Install SVIM-asm using Pip

Source: https://github.com/eldariont/svim-asm/blob/master/README.rst

Alternative installation method using pip after cloning the repository. Requires Python 3.

```bash
#Install from github (requires Python 3)
git clone https://github.com/eldariont/svim-asm.git
cd svim-asm
pip install .
```

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

### Install SVIM-asm using Conda

Source: https://github.com/eldariont/svim-asm/blob/master/README.rst

Recommended method for installing SVIM-asm into a new or existing conda environment. This ensures proper dependency management.

```bash
#Recommended: Install via conda into a new environment
conda create -n svimasm_env --channel bioconda svim-asm

#Alternatively: Install via conda into existing (active) environment
conda install --channel bioconda svim-asm
```

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

### Align and Analyze Haploid Assembly with SVIM-asm

Source: https://github.com/eldariont/svim-asm/blob/master/README.rst

This sequence demonstrates how to align a haploid assembly to a reference genome using minimap2, sort the alignments with samtools, and then call structural variants using SVIM-asm.

```bash
minimap2 -a -x asm5 --cs -r2k -t <num_threads> <reference.fa> <assembly.fasta> > <alignments.sam>
samtools sort -m4G -@4 -o <alignments.sorted.bam> <alignments.sam>
samtools index <alignments.sorted.bam>
svim-asm haploid <working_dir> <alignments.sorted.bam> <reference.fa>
```

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

### Align and Analyze Diploid Assembly with SVIM-asm

Source: https://github.com/eldariont/svim-asm/blob/master/README.rst

This process shows how to align both haplotypes of a diploid assembly to a reference genome, sort the alignments, index them, and then use SVIM-asm to call structural variants.

```bash
minimap2 -a -x asm5 --cs -r2k -t <num_threads> <reference.fa> <haplotype1.fasta> > <alignments_hap1.sam>
minimap2 -a -x asm5 --cs -r2k -t <num_threads> <reference.fa> <haplotype2.fasta> > <alignments_hap2.sam>
samtools sort -m4G -@4 -o <alignments_hap1.sorted.bam> <alignments_hap1.sam>
samtools sort -m4G -@4 -o <alignments_hap2.sorted.bam> <alignments_hap2.sam>
samtools index <alignments_hap1.sorted.bam
samtools index <alignments_hap2.sorted.bam
svim-asm diploid <working_dir> <alignments_hap1.sorted.bam> <alignments_hap2.sorted.bam> <reference.fa>
```

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