Metadata-Version: 2.1
Name: RagTag
Version: 1.0.0
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: # 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=ff69b4)
        
        
        #### Reference-guided genome assembly correction and scaffolding. RagTag is the successor to RaGOO.
        
        ## Getting Started
        
        ```bash
        git clone https://github.com/malonge/RagTag
        cd RagTag
        python3 setup.py install
        
        # correct contigs
        ragtag.py correct ref.fasta query.fasta
        
        # scaffold contigs
        ragtag.py scaffold ref.fa ragtag_output/query.corrected.fasta
        ```
        
        ## Dependencies
        - [Minimap2](https://github.com/lh3/minimap2) or [Nucmer](http://mummer.sourceforge.net/)
        - Python 3 (with the following auto-installed packages)
            - numpy
            - intervaltree
            - pysam
            
        ## 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.
        
        ## \*More Docs Soon\*
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
