Metadata-Version: 1.0
Name: XYalign
Version: 1.1.2
Summary: Command line tools and python library to infer ploidy, correct for sex chromosome complement, and work with NGS data
Home-page: https://github.com/WilsonSayresLab/XYalign
Author: Tim Webster
Author-email: twebster17@gmail.com
License: GNU General License version 3
Description: <p align="center">
          <img src="https://github.com/WilsonSayresLab/XYalign/blob/master/Files/XYlogo.png" width="500"/>
        </p>
        
        # XYalign: Inferring Sex Chromosome Ploidy in NGS Data
        Timothy H. Webster, Madeline Couse, Bruno Grande, Eric Karlins, Tanya Phung, Phillip Richmond, Whitney Whitford, Melissa A. Wilson Sayres
        
        ## Background
        The high degree of similarity between gametologous sequences on the sex chromosomes can lead to the misalignment of sequencing reads and substantially affect variant calling. Here we present XYalign, a new tool that (1) quickly infers sex chromosome ploidy in NGS data, (2) remaps reads based on the inferred sex chromosome complement of the individual, and (3) outputs quality, depth, and allele-balance metrics across chromosomes.
        
        [October 17, 2016 slide show of concept and inital results for Hackseq](https://docs.google.com/presentation/d/1OB2d_mu5zC742N_NKfzHjVpUm4BFtm5lUzniLLI--OQ/edit?usp=sharing)
        
        [November 18, 2016 poster presentation for the Evolutionary Genomics of Sex 2016 Meeting](https://figshare.com/articles/XYalign_Inferring_and_Correcting_for_Sex_Chromosome_Ploidy_in_Next-Generation_Sequencing_Data/4292924/1)
        
        ## Using XYalign
        
        See full documentation at [Read The Docs](http://xyalign.readthedocs.io/en/latest/index.html)
        
        Post any questions you have at the [XYalign Google Group](https://groups.google.com/forum/#!forum/xyalign)
        
        ## If you cloned XYalign before April 5, 2017 please clone a fresh version
        On April 5th, we removed a host of large files using BFG Repo Cleaner, which changed
        the commit history of the repo.  Because of this, ```git pull``` will no longer work on clones
        prior to this cleaning.  Therefore, if you cloned before this date (or can't remember when you
        cloned), it's probably a good idea to clone a fresh version.
        
        ## Group Members
        Name | email | github ID
        --- | --- |  ---
        Tim Webster | timothy.h.webster@asu.edu | @thw17
        Madeline Couse| mhcouse@gmail.com | @Madelinehazel
        Bruno Grande | bgrande@sfu.ca | @brunogrande
        Eric Karlins | karlinser@mail.nih.gov | @ekarlins
        Tanya Phung | tnphung@ucla.edu | @tnphung
        Phillip Richmond | phillip.a.richmond@gmail.com | @Phillip-a-Richmond
        Whitney Whitford | whitney.whitford@auckland.ac.nz | @whitneywhitford
        Melissa A. Wilson Sayres | melissa.wilsonsayres@asu.edu | @mwilsonsayres
        
Platform: UNKNOWN
