Metadata-Version: 2.4
Name: captus
Version: 1.6.2
Summary: Tools for hybridization capture-based target enrichment: Probe Design, Data Assembly, Marker Extraction and Alignment
Home-page: https://github.com/edgardomortiz/Captus
Author: Edgardo M. Ortiz
Author-email: e.ortiz.v@gmail.com
License: GPL
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license
Dynamic: license-file
Dynamic: summary

<p align="center">
  <img src=docs/static/images/logo.svg alt=captus_logo width=500>
</p>

### *Assembly of Phylogenomic Datasets from High-Throughput Sequencing data*

Documentation: [https://edgardomortiz.github.io/captus.docs](https://edgardomortiz.github.io/captus.docs)

[![Install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/captus/README.html)
[![Bioconda downloads](https://anaconda.org/bioconda/captus/badges/downloads.svg)](https://anaconda.org/bioconda/captus)
[![Version in Bioconda](https://anaconda.org/bioconda/captus/badges/version.svg)](https://anaconda.org/bioconda/captus)
[![Last updated](https://anaconda.org/bioconda/captus/badges/latest_release_date.svg)](https://github.com/edgardomortiz/Captus/releases)

## INSTALLATION

### Using conda/mamba (recommended)

`Captus` is available as a [conda package](https://anaconda.org/bioconda/captus). If you have [`conda`](https://docs.conda.io/projects/conda/en/latest/index.html) or [`mamba`](https://mamba.readthedocs.io/en/latest/index.html) installed, you can easily create a new environment and install `Captus` with all dependencies using the following command:

#### _Linux:_
```shell
conda create -n captus -c bioconda -c conda-forge captus
```
or
```shell
mamba create -n captus -c bioconda -c conda-forge captus
```

#### _Mac computers with Intel processors:_
```shell
conda create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0
```
or
```shell
mamba create -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0
```

#### _Mac computers with Apple silicon (M processors):_
```shell
conda create --platform osx-64 -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 mmseqs2=16.747c6
```
or
```shell
mamba create --platform osx-64 -n captus -c bioconda -c conda-forge captus megahit=1.2.9=hfbae3c0_0 mmseqs2=16.747c6
```

Then check that `Captus` was correctly installed:

```shell
conda activate captus
captus -h
```

If the program was correctly installed, you will see the following help message:

```text
usage: captus command [options]

Captus 1.6.2: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Captus-assembly commands:
  command     Program commands (in typical order of execution)
                clean = Trim adaptors and quality filter reads with BBTools,
                        run FastQC on the raw and cleaned reads
                assemble = Perform de novo assembly with MEGAHIT and estimate
                           contig depth of coverage with Salmon. Assembling
                           reads that were cleaned with the 'clean' command is
                           recommended, but reads cleaned elsewhere are also
                           allowed
                extract = Recover targeted markers with BLAT and Scipio:
                          Extracting markers from the assembly obtained with
                          the 'assemble' command is recommended, but any other
                          assemblies in FASTA format are also allowed
                align = Align extracted markers across samples with MAFFT or
                        MUSCLE: Marker alignment depends on the directory
                        structure created by the 'extract' command. This step
                        also performs paralog filtering and alignment trimming
                        using TAPER and ClipKIT

Help:
  -h, --help  Show this help message and exit
  --version   Show Captus' version number

For help on a particular command: captus_assembly command -h
```

### Manual installation

If you are unable to use `conda`/`mamba` for any reason, you will need to install all dependencies manually. Please refer to the [documentation](https://edgardomortiz.github.io/captus.docs/basics/installation/#manual-installation) for details.

## USAGE

Documentation and tutorials are available at [https://edgardomortiz.github.io/captus.docs](https://edgardomortiz.github.io/captus.docs)

> [!TIP]
>
> ### Extract BUSCO
>
> Since v1.0.1, `Captus` supports the use of any BUSCO lineage dataset as reference targets for extraction. Just download one of the `.tar.gz` files from [https://busco-data.ezlab.org/v5/data/lineages](https://busco-data.ezlab.org/v5/data/lineages) and provide the path to `captus extract`.
>
> For example:
>
> ```text
> captus extract -a 02_assemblies -n ~/Downloads/aves_odb10.2021-02-19.tar.gz
> ```

## CITATION

Ortiz, E.M., A. Höwener, G. Shigita, M. Raza, O. Maurin, A. Zuntini, F. Forest, W.J. Baker, H. Schaefer. (2023). *A novel phylogenomics pipeline reveals complex pattern of reticulate evolution in Cucurbitales*. bioRxiv [https://doi.org/10.1101/2023.10.27.564367](https://doi.org/10.1101/2023.10.27.564367)
