---
tags:
  - Free
catalog:
  name: Diamond
  description: Sequence similarity search tool for proteins and nucleotides
  license_type: Free
  disciplines:
    - Biosciences
  available_on:
    - Puhti
---

# Diamond

Diamond is a fast sequence similarity search tool for matching nucleotide or protein sequences against protein databases.
The key features of Diamond are:

* Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST.
* Frameshift alignments for long read analysis.
* Low resource requirements and suitable for running on standard desktops or laptops.
* Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.

[TOC]

## License

Free to use and open source under [GNU AGPLv3](https://www.gnu.org/licenses/agpl-3.0.en.html).

## Available

* Puhti: 2.0.15, 2.1.6, 2.1.10

## Usage

To use Diamond, run first the command:

```bash
module load biokit
```

or:

```bash
module load diamond
```

To load a specific version, e.g:

```bash
module load diamond/2.0.15
```

After that, you can check the Diamond help with the command:

```bash
diamond help
```

CSC provides Diamond indexes for SwissProt (swiss), Uniprot (uniprot) and NCBI non-redundant databases (nr). Location of these databases is defined with the environment variable `$DIAMONDDB`. For example, searching hits for a set of nucleotide sequences from the SwissProt database could be done with the command:

```bash
diamond blastx --query nuc.fasta -d $DIAMONDDB/swiss --out diamond_results.txt -p 4 --max-target-seqs 500
```

You can also do searches against your own protein sequence database. In this case, you must first calculate Diamond indexes for your reference protein set with command `diamond makedb`. For example:

```bash
diamond makedb --in refrerence_proteins.fasta -d my_ref -p 4
```

The command above creates a Diamond index file (`my_ref.dmnd`) that can be used as the query database:

```bash
diamond blastx --query nuc.fasta -d my_ref --out diamond_results2.txt -p 4 --max-target-seqs 500
```

## More information

* [Diamond Github page](https://github.com/bbuchfink/diamond)
