obitools4/README.md

# obitools V4

*OBITools V4* is the new version of *OBITools*. They are closer to *OBITools2* than to *OBITools3*.
They are implemented in *GO* and are tens of times faster than OBITools2.

The git for *OBITools4* is available at :

> https://github.com/metabarcoding/obitools4

## Installing *OBITools V4*

An installation script that compiles the new *OBITools* on your Unix-like system is available online.
The easiest way to run it is to copy and paste the following command into your terminal

```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash
```

By default, the script installs the latest version of *OBITools* commands and other associated files into the `/usr/local` directory.

### Installation Options

The installation script offers several options:

>  -l, --list              List all available versions and exit.
> 
>  -v, --version           Install a specific version (e.g., `-v 4.4.3`).
>                          By default, the latest version is installed.
> 
>  -i, --install-dir       Directory where obitools are installed 
>                          (as example use `/usr/local` not `/usr/local/bin`).
> 
>  -p, --obitools-prefix   Prefix added to the obitools command names if you
>                          want to have several versions of obitools at the
>                          same time on your system (as example `-p g` will produce
>                          `gobigrep` command instead of `obigrep`).
>
>  -j, --jobs              Number of parallel jobs used for compilation
>                          (default: 1). Increase this value to speed up
>                          compilation on multi-core systems (e.g., `-j 4`).

### Examples

List all available versions:
```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --list
```

Install a specific version:
```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash -s -- --version 4.4.3
```

Install in a custom directory with command prefix:
```{bash}
curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | \
      bash -s -- --install-dir test_install --obitools-prefix k
```

In this last example, the binaries will be installed in the `test_install` directory and all command names will be prefixed with the letter `k`. Thus, `obigrep` will be named `kobigrep`.

### Note on Version Compatibility

The names of the commands in the new *OBITools4* are mostly identical to those in *OBITools2*.
Therefore, installing the new *OBITools* may hide or delete the old ones. If you want both versions to be 
available on your system, use the `--install-dir` and `--obitools-prefix` options as shown above.

## Continuing the analysis...

Before with _OBITools2_ to continue the analysis, `obitab` was used as last command to produce a tab delimited file that was loadable in R or in any spreadsheet. The generated file was huge and required to load the full dataset in memory to be produced. Hereby _OBITools4_ proposes to substitute the `obitab` usage by the [ROBIFastRead](https://git.metabarcoding.org/obitools/obitools4/robireadfasta) R module.