Metadata-Version: 2.4
Name: tasmanian-mismatch
Version: 1.1.1
Summary: Tasmanian tool to analyze mismatches at read and position in high throughput sequencing data
Home-page: https://github.com/nebiolabs/tasmanian-mismatch
Author: Ariel Erijman and Brad Langhorst
Author-email: Ariel Erijman <aerijman@neb.com>, Brad Langhorst <blanghorst@neb.com>
License: GNU
Project-URL: Homepage, https://github.com/nebiolabs/tasmanian-mismatch
Project-URL: Repository, https://github.com/nebiolabs/tasmanian-mismatch
Project-URL: Issues, https://github.com/nebiolabs/tasmanian-mismatch/issues
Keywords: sequencing,bioinformatics,mismatch,analysis
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENCE.txt
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: plotly
Dynamic: author
Dynamic: home-page
Dynamic: license-file
Dynamic: requires-python

[![Bioconda](https://img.shields.io/conda/dn/bioconda/fgbio.svg?label=Bioconda)](http://bioconda.github.io/recipes/fgbio/README.html)
[![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)
[![Language](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org)

![Image of Tasmanian Devil](https://upload.wikimedia.org/wikipedia/commons/thumb/4/43/Sarcophilus_harrisii_taranna.jpg/512px-Sarcophilus_harrisii_taranna.jpg)

Tasmanian
====
    
A tool for the analysis of reference mismatches in high throughput sequencing data from DNA samples. Unlike other tools, it is able to evalutate the portions of reads that overlap with specified regions (e.g. Repeats)


<!---toc start-->
  * [Goals](#goals)
  * [Install](#install)
  * [Contributing](#contributing)
  * [Authors](#authors)
  * [License](#license)

<!---toc end-->

# Install
conda: `conda install -c bioconda tasmanian-mismatch`  
pip:   `pip install tasmanian-mismatch`


# Goals

The main goal is to identify systematic missmatches that might confound SNPs or other variations that should or should not be associated to biological outcomes. Since we noticed a set of regions, which might not necessarily be missplaced in the reference genome, have dramatic effects in this analysis, we provide a way of spliting these reads and incorporate the information in different tables, so that intersecting/non intersecting reads are not filtered out. Also, the researcher has a more accurate picture of the influence of these regions in the observed artifacts.

### Overview of Tasmanian use:

```bash
samtools view bam | run_intersections [OPTIONS] | run_tasmanian [OPTIONS]
```

1. Classification of each base of the read into overlapping (in which case could be contained or boundary - see figure below) or Non-overlapping with regions of interest included in a bed/bedgraph file.
2. Positional analysis of artifacts splitted by read 1 and read 2.

<img src="figures/intersections_tasmanian.jpg"/>
---

### The output includes tables to manupulate and plot the data and a built in report for fast access the data (see figure below).
<img src="figures/snapshot_good.jpg"/>


* Easy to use command-line and [nextflow](https://www.nextflow.io/) implementation.
* Includes a [Galaxy](https://toolshed.g2.bx.psu.edu/) wrapper 


## Contributing

Contributions are welcome and encouraged.

## Running Tests

To run the test suite for Tasmanian, follow these steps:

1. Create a virtual environment:
  ```
  python3.10 -m venv tasmanian_venv
  source tasmanian_venv/bin/activate
  ```

2. Install dependencies:
  ```
  pip install -r requirements.txt
  ``` 

3. Run the tests:
  ```
  bash tasmanian/tests/basic_tests.sh
  ```

## Authors

* [Brad Langhorst](https://github.com/bwlang)
* [Ariel Erijman](https://github.com/aerijman)

## License

`tasmanian artifact metrics tool` is open source software released under the [GNU License](LICENCE.txt).

