Metadata-Version: 2.1
Name: captus
Version: 0.9.88
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
Description-Content-Type: text/markdown
License-File: LICENSE.txt

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

The simplest way to install `Captus` is to create an isolated software environment using `conda`,
if you don't have `conda` we recommend to install [`miniconda`](https://docs.conda.io/en/latest/miniconda.html). Once you have `conda` installed in your system you can run:

```bash
conda create -n captus -c bioconda -c conda-forge captus
```
Then activate the `conda` environment you created:

```bash
conda activate captus
```
Finally, test that `Captus` was correctly installed:
```bash
captus_assembly
```


And if the program was correctly installed you will see the main help page of Captus:
```text
usage: captus_assembly command [options]

Captus 0.9.88: 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: 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: Marker
                        alignment depends on the directory structure created by the
                        'extract' command. This step also performs paralog filtering
                        and alignment trimming using 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

ERROR: Missing command
```

## Usage

Documentation and tutorials available at https://edgardomortiz.github.io/captus.docs/
