Metadata-Version: 2.1
Name: RagTag
Version: 2.0.0
Summary: Fast reference-guided genome assembly scaffolding
Home-page: https://github.com/malonge/RagTag
Author: Michael Alonge
Author-email: malonge11@gmail.com
License: MIT
Description: ![logo_text](logo/logo_banner.svg)
        
        ## RagTag 
        
        [![DOI](https://zenodo.org/badge/242898323.svg)](https://zenodo.org/badge/latestdoi/242898323) [![RELEASE](https://img.shields.io/github/v/release/malonge/RagTag?color=EE7733)](https://github.com/malonge/RagTag/releases/tag/v2.0.0) [![CONDA](https://img.shields.io/conda/dn/bioconda/ragtag?color=009988&label=conda)](https://anaconda.org/bioconda/ragtag) [![GitHub](https://img.shields.io/github/license/malonge/RagTag?color=CC3311)](https://github.com/malonge/RagTag/blob/master/LICENSE)
        
        RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. Tasks include:
        
        - Homology-based misassembly [correction](https://github.com/malonge/RagTag/wiki/correct)
        - Homology-based assembly [scaffolding](https://github.com/malonge/RagTag/wiki/scaffold) and [patching](https://github.com/malonge/RagTag/wiki/patch)
        - Scaffold [merging](https://github.com/malonge/RagTag/wiki/merge)
          
        Ragtag also provides [command line utilities](https://github.com/malonge/RagTag/wiki/Usage) for working with common genome assembly file formats.
        
        ![logo_text](logo/descriptive_diagram.svg)
        
        ## Getting Started
        
        ```bash
        # install with conda
        conda install -c bioconda ragtag
        
        # correct a query assembly
        ragtag.py correct ref.fasta query.fasta
        
        # scaffold a query assembly
        ragtag.py scaffold ref.fasta query.fasta
        
        # scaffold with multiple references/maps
        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 other.map.agp
        
        # use Hi-C to resolve conflicts
        ragtag.py merge -b hic.bam query.fasta out_*/*.agp other.map.agp
        
        # make joins and fill gaps in target.fa using sequences from query.fa
        ragtag.py patch target.fa query.fa
        ```
        
        ## Docs
        Please see the [Wiki](https://github.com/malonge/RagTag/wiki) for detailed documentation.
        
        ## Dependencies
        - [Minimap2](https://github.com/lh3/minimap2), [Unimap](https://github.com/lh3/unimap), 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. <br>https://doi.org/10.1186/s13059-019-1829-6
        
        ## 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). [Luca Venturini](https://github.com/lucventurini) 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. RagTag "patch" was inspired by [Grafter](https://github.com/mkirsche/Grafter), a scaffolding tool written by [Melanie Kirsche](https://github.com/mkirsche). Melanie provided guidance for the RagTag implementation. [Michael Schatz](http://schatz-lab.org/) has provided guidance for the whole project.   
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
