# Quickstart

## Installing mOTUs

Installing via conda is recommended as conda will automatically take care of installing all the dependencies. 

```bash
#recommended to install motus in a new environment
conda create -n motus-env
conda install -n motus-env -c bioconda motus
```

You can check if the installation was successful with:

```bash
motus profile --test
```

Please check [Installation]("documentation/install.md") for more detailed instructions and other installation options (`pip` and `github`).

## Profiling a single sample

You can use the `motus profile` command to create a taxonomic profile from a metagenomic sample consisting of one or more fastq files. See [Tutorial](documentation/tutorial.md) for more detailed instructions with a specific example. 

```bash
#profiling with forward, reverse and unpaired reads
motus profile -f for_sample.fastq -r rev_sample.fastq -s no_pair.fastq -t 4 -n test_sample -o taxonomy_profile.txt
```
`-f`, input fastq file(s) in forward orientation


`-r`, input fastq files(s) in reverse orientation


`-s`, input fastq file(s) with unpaired reads


`-t`, number of threads to use (we recommended using 4 or 8 threads)


`-n`, identifier name of the resulting profile, this will be use for the header of the table during the merging step


`-o`, file to save the result to

To fine-tune the algorithm parameters (e.g. precision and recall) and modify the result format, refer to the [Tutorial](documentation/tutorial.md) and [Command manual](documentation/options_manual.md)

## Merging multiple profiles

Using the `motus merge` command, you can easily merge the profiles of multiple samples

```bash
#merging profiles of sample A and sample B
motus merge -i sampleA.motus,sampleB.motus -o merged.motus

#merging all profiles within a directory DIR
motus merge -d DIR -o merged.motus
```

> For a more comprehensive tutorial with practical examples, visit this [link](documentation/tutorial.md). For a description of all command options, click [here](documentation/options_manual.md).