Metadata-Version: 1.2
Name: dupliganger
Version: 0.92
Summary: A reference-based, UMI-aware, 5ʹ-trimming-aware PCR duplicate removal pipeline.
Home-page: https://github.com/uoregon-postlethwait/dupliganger
Author: Postlethwait Lab, University of Oregon
Author-email: postlethwait.lab@gmail.com
License: LICENSE.txt
Project-URL: Source, https://github.com/uoregon-postlethwait/dupliganger
Project-URL: Bug Reports, https://github.com/uoregon-postlethwait/dupliganger/issues
Description: Dupligänger
        ===========
        
        *Dupligänger* is a reference-based, UMI-aware, 5'-trimming-aware PCR duplicate
        removal pipeline.
        
        Usage: dupliganger [options] <command> [<args>...]
        
        
        *Dupligänger* is a pipeline.  Each stage of the pipeline is run by passing a
        'command' to *Dupligänger*.  The commands / pipeline-steps (in order) are as
        follows::
        
           remove-umi         1. Annotate read names with UMIs (clip inline UMIs if needed).
           remove-adapter     2. Remove adapters ('Cutadapt' wrapper).
           qtrim              3. Quality trim ('Trimmomatic' wrapper).
           annotate-qtrim     4. Annotates quality trimmed file(s).
           align              5. Align reads to a reference genome assembly (performed manually by user).
           dedup              6. Use the alignment to remove PCR duplicates.
        
        While generally used only by the developers of *Dupligänger*, the 'dedup'
        command is comprised of the following *Dupligänger* commands run in the
        following order::
        
            build-read-db      1. Build a database of aligned reads.
            build-location-db  2. Build a database of locations of aligned reads.
            build-dup-db       3. Build a database of PCR duplicates.
        
        Options::
        
            -o OUT_DIR      Place results in directory OUT_DIR.
            --compress      Compress output.
        
        Note:
            *Dupligänger* supports (and autodetects) input FASTQ files that are gzipped.
        
        See 'dupliganger help <command>' for more information on a specific command.
        
        Documentation
        =============
        
        For further information on *Dupligänger*, please see the full documentation at
        https://github.com/uoregon-postlethwait/dupliganger
        
        Authors
        =======
        
        * Jason Sydes - Conceptual Design and Software Engineering
        * Peter Batzel - Conceptual Design
        * John H. Postlethwait - Project Advisor
        
        Funding
        =======
        
        *Dupligänger* has been funded by the following grants:
        
        * NIH R01 OD011116 - Resources for Teleost Gene Duplicates and Human Disease
        * NIH R24 OD011199 - Advancing the Scientific Potential of Transcriptomics in Aquatic Models
        * NIH R24 OD018555 - Development of Aquatic Model Resources for Therapeutic Screens
        * NSF PLR-1543383 - Antarctic Fish and MicroRNA Control of Development and Physiology 
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: Free for non-commercial use
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: >=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4
