Metadata-Version: 2.4
Name: paleomix
Version: 1.4.0
Summary: Bioinformatics pipelines for HTS data
Project-URL: Homepage, https://github.com/MikkelSchubert/paleomix
Project-URL: Documentation, https://paleomix.readthedocs.io
Project-URL: Repository, https://github.com/MikkelSchubert/paleomix.git
Project-URL: Issues, https://github.com/MikkelSchubert/paleomix/issues
Author-email: Mikkel Schubert <MikkelSch@gmail.com>
License: Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Keywords: bam,bioinformatics,hts,pipeline
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Requires-Dist: coloredlogs>=10.0
Requires-Dist: configargparse>=0.13.0
Requires-Dist: pysam>=0.10.0
Requires-Dist: ruamel-yaml>=0.16.0
Requires-Dist: setproctitle>=1.1.0
Description-Content-Type: text/x-rst

**********************
The PALEOMIX pipelines
**********************

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

----------------------
Installation and usage
----------------------

Detailed instructions can be found in the `documentation <http://paleomix.readthedocs.io/>`_ for PALEOMIX. For questions, bug reports, and/or suggestions, please use the `GitHub tracker <https://github.com/MikkelSchubert/paleomix/issues/>`_ or contact Mikkel Schubert at `MikkelSch@gmail.com <mailto:MikkelSch@gmail.com>`_.


---------
Citations
---------

The PALEOMIX pipelines have been published in Nature Protocols; if you make use of PALEOMIX in your work, then please cite

  Schubert M, Ermini L, Sarkissian CD, Jónsson H, Ginolhac A, Schaefer R, Martin MD, Fernández R, Kircher M, McCue M, Willerslev E, and Orlando L. "**Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX**". Nat Protoc. 2014 May;9(5):1056-82. doi: `10.1038/nprot.2014.063 <http://dx.doi.org/10.1038/nprot.2014.063>`_. Epub 2014 Apr 10. PubMed PMID: `24722405 <http://www.ncbi.nlm.nih.gov/pubmed/24722405>`_.

The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite

  Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2017 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_.
