Metadata-Version: 1.2
Name: amplimap
Version: 0.3
Summary: amplicon/smMIP mapping and analysis pipeline
Home-page: https://github.com/koelling/amplimap/
Author: Nils Koelling
Author-email: git@nk.gl
License: Apache License, Version 2.0
Download-URL: https://github.com/koelling/amplimap/archive/v0.3.tar.gz
Description: .. image:: https://raw.githubusercontent.com/koelling/amplimap/master/amplimap_logo_400px.png
        	:width: 400px
        
        ==========================================================
        amplimap: amplicon mapping and analysis pipeline
        ==========================================================
        
        
        amplimap is a pipeline to process and analyse short-read sequencing
        data from **smMIP-panels** or **PCR-based amplicons**. It was designed
        to support both **germline variant calling** as well as **quantification of
        variant allele frequencies** using ultra-high-coverage pileups with and without
        **UMIs**.
        
        amplimap takes fastq or bam files generated from an Illumina
        sequencer (tested with MiSeq, HiSeq, and NextSeq), assigns each read pair to a
        probe/amplicon, trims and aligns the reads and then generates a set of
        basic statistics. After that, two different types of analyses can be
        performed:
        
        1. Germline variant calling using Platypus/GATK and annotation with Annovar,
           to generate an annotated table of potentially
           pathogenic variants.
        
        2. Per-basepair “pileup” of reads to generate nucleotide counts of
           each base at each target basepair and each sample, for analysis of
           allele frequencies.
        
        Built on top of Snakemake and Python 3, amplimap is entirely
        automated and can be run on a single machine as well as on a HPC cluster
        (eg. LSF, SGE).
        
        Links
        --------
        
        - Package: https://pypi.org/project/amplimap/
        - Code: https://github.com/koelling/amplimap/
        - Documentation: https://amplimap.readthedocs.io/
        
        
        Basic installation
        -------------------
        ::
        
        	pip install amplimap
        
        Requires Python 3.5+
Keywords: amplimap amplicon smmip mapping analysis pipeline
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: MacOS
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3
