# isONclust3
A rust implementation of a novel de novo clustering algorithm.
isONclust3 is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene family. Output is a tsv file with each read assigned to a cluster-ID and a folder 'fastq' containing one fastq file per cluster generated. Detailed information is available in the isONclust3 paper.

# Table of contents
1. [Installation](#installation)
2. [Output](#output)
3. [Running isONclust3](#Running)
4. [Contact](#contact)
5. [Credits](#credits)

## Installation Guide <a name="installationguide"></a>
At the moment building from source is the only option to install the tool. This requires users to install the Rust programming language onto their system.

## Installing Rust <a name="installingrust"></a>
You can install rust via<br />

`curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh` (for macOS and Linux or other Unix-based OS). For Windows please follow the instructions on the following site: https://forge.rust-lang.org/infra/other-installation-methods.html .<br />

## Installation <a name="installation"></a>
After cloning the repository via `git clone https://github.com/aljpetri/isONclust3.git` use the following two commands to compile the code: <br />
`cd isONclust3` <br />
`cargo build --release` ( Compile the current package, the executable is then located in target/release) <br />


## Running isONclust3 <a name="Running"></a>
IsONclust3 can be used on either Pacbio data or ONT data. 

```
isONclust3 --fastq {input.fastq} --mode ont  --outfolder {outfolder}         # Oxford Nanopore reads
isONclust3 --fastq {input.fastq} --mode pacbio  --outfolder {outfolder}      # PacBio reads

```

The `--mode ont` argument means setting `--k 13 --w 21`. The `--mode pacbio` argument is equal to setting `--k 15 --w 51`.

## Output <a name="output"></a>

#### Clustering information
The output consists of a tsv file `final_clusters.tsv` present in the specified output folder. In this file, the first column is the cluster ID and the second column is the read accession. For example:
```
0 read_X_acc
0 read_Y_acc
...
n read_Z_acc
```
if there are n reads there will be n rows. Some reads might be singletons.
### Clusters
IsONclust outputs the reads in .fastq file format with each file containing the reads for the respective cluster. The .fastq files are located in the `fastq_files` directory that is created in the given outfolder.

## Contact <a name="contact"></a>
If you encounter any problems, please raise an issue on the issues page, you can also contact the developer of this repository via:
alexander.petri[at]math.su.se


## Credits <a name="credits"></a>