Metadata-Version: 2.1
Name: RagTag
Version: 1.1.0
Summary: Fast reference-guided genome assembly scaffolding
Home-page: https://github.com/malonge/RagTag
Author: Michael Alonge
Author-email: malonge11@gmail.com
License: MIT
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: intervaltree
Requires-Dist: numpy
Requires-Dist: pysam
Requires-Dist: networkx

[![DOI](https://zenodo.org/badge/242898323.svg)](https://zenodo.org/badge/latestdoi/242898323) [![RELEASE](https://img.shields.io/github/v/release/malonge/RagTag?color=ff69b4)](https://github.com/malonge/RagTag/releases/tag/v1.1.0) [![CONDA](https://img.shields.io/conda/dn/bioconda/ragtag?color=%230BE67&label=conda)](https://anaconda.org/bioconda/ragtag)


![logo_text](logo/ragtag_logo_text.svg)

## Getting Started

```bash
# install with conda
conda install -c bioconda ragtag

# correct contigs
ragtag.py correct ref.fasta query.fasta

# scaffold contigs
ragtag.py scaffold ref.fa ragtag_output/query.corrected.fasta

# scaffold with multiple references
ragtag.py scaffold -o out_1 ref1.fasta query.fasta
ragtag.py scaffold -o out_2 ref2.fasta query.fasta
ragtag.py merge query.fasta out_*/*.agp

# use Hi-C to resolve conflicts
ragtag.py merge -b hic.bam query.fasta out_*/*.agp
```

## Docs
Please see the [Wiki](https://github.com/malonge/RagTag/wiki) for detailed documentation.

## Dependencies
- [Minimap2](https://github.com/lh3/minimap2) or [Nucmer](http://mummer.sourceforge.net/)
- Python 3 (with the following auto-installed packages)
    - numpy
    - intervaltree
    - pysam
    - networkx

## Citation

Alonge, Michael, et al. ["RaGOO: fast and accurate reference-guided scaffolding of draft genomes."](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1829-6) Genome biology 20.1 (2019): 1-17.

## Acknowledgments

Many of the major algorithmic improvements relative to RaGOO's first release were provided by Aleksey Zimin, lead developer of the [MaSuRCA assembler](https://github.com/alekseyzimin/masurca). This includes the use of read-mapping for misassembly validation as well as the use of alignment merging for improved scaffolding. [Luca Venturini](https://github.com/lucventurini) also suggested and initially implemented many feature enhancments, such as pysam integration. RagTag "merge" was inspired by [CAMSA](https://doi.org/10.1186/s12859-017-1919-y). The developer of CAMSA, [Sergey Aganezov](https://github.com/aganezov), helped review relevant RagTag code.  


