Metadata-Version: 1.0
Name: mirror-seq
Version: 0.2.2
Summary: The bioinformatics tool for Mirror-seq.
Home-page: https://github.com/Zymo-Research/mirror-seq
Author: Hunter Chung
Author-email: b89603112@gmail.com
License: Apache License 2.0
Description: What is it
        ==========
        
        Mirror-seq is a assay invented by `Zymo
        Research <http://zymoresearch.com>`__ to detect
        `hydroxymethylation <>`__ (hmc) in genomes using `bisulfite
        sequencing <>`__. This analysis tool helps biologists to analyze
        sequencing data. It takes Fastq files from sequencers and generate
        hydroxymethylation ratio for each CpGs.
        
        What's included
        ===============
        
        We provide two way to do analysis. If you are new or like to do a quick
        analysis, the **Qucik Start** below is the total solution you would
        like. It set up the environment for you and has a simple workflow -
        trimming, alignment, hydroxymethylation calling. Just type in one
        command. You will find results in your workplace in several hours.
        
        If you are bioinformatics expert or anyone eager to try different
        parameters, we also provide the component of initial fill-in nucleotides
        trimming () and the final hydroxymethylation calling () parts as
        standalone program. You can plug in your favor QC and adapter trimming
        software and alignment software with your homemade parameters. Please
        fellow the **installation** section below for more details.
        
        Quick Start
        ===========
        
        We created a `Docker <>`__ image to solve the dependency problem and
        scientists can use either Windows, MacOS, or Linux to run the analysis.
        
        Install Docker
        --------------
        
        Find your OS and follow the installation instructions of
        `Windows <https://docs.docker.com/windows/step_one/>`__,
        `MacOS <https://docs.docker.com/mac/step_one/>`__, and
        `Linux <https://docs.docker.com/linux/step_one/>`__ from Docker's
        official website.
        
        Run Mirror-seq
        --------------
        
        You need to create a workplace directory (``<YOUR WORKPLACE>``) and put
        the following files inside: \* Read 1 and Read 2 Fastq files. \* Genome
        index (We provide `human index <>`__. Unzip the file after downloading.)
        
        ::
        
            docker run -it --rm -v <YOUR WORKPLACE>:/workplace \
              zymoresearch/mirror-seq \
              -1 <READ 1 FILENAME> -2 <READ 2 FILENAME> \
              -g <GENOME INDEX FOLDER NAME> --bed
        
        Notes:
        ------
        
        Although it is super easy to run the analysis tool, there are several
        things you need to know in order to run it smoothly. \* The alignment
        part is memory intensive and CPU intensive.
        `Bismark <http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/>`__,
        the aligner we used in our tool, suggests at least 5 cores and > 16GB of
        RAM. \* Usually Fastq files are several GB even with compression. In the
        first trimming part, the tool could need up to 3 times large as the
        original input. Please make sure your workplace has enough storage
        space.
        
        installation
        ============
        
        Dependencies
        ============
        
        Python (2.7)
        ------------
        
        -  `NumPy <http://www.numpy.org/>`__: 1.7.0
        -  `pandas <http://pandas.pydata.org/>`__: 0.18.0
        -  `numexpr <https://github.com/pydata/numexpr>`__: 2.5.2
        -  `pysam <http://pysam.readthedocs.org/en/latest/api.html>`__: 0.9.0
        -  `cutadapt <http://cutadapt.readthedocs.org/en/stable/guide.html>`__:
           1.9.1
        -  `PyTables <http://www.pytables.org/>`__: 3.2.2
        
        Bioinformatics software
        -----------------------
        
        -  `bedToBigBed <http://hgdownload.cse.ucsc.edu/admin/exe/>`__
        -  `bedSort <http://hgdownload.cse.ucsc.edu/admin/exe/>`__
        -  `Trim
           Galore! <http://www.bioinformatics.bbsrc.ac.uk/projects/trim_galore/>`__:
           0.3.7
        -  `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`__:
           2.2.6
        -  `Bismark <http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/>`__:
           0.14.5
        
Keywords: mirror sequencing next-gen hydroxymethylation bisulfite bioinformatics
Platform: UNKNOWN
