Update README.md to include reason for AMD exclusivity.

Bacteria methylate their DNA in three ways: 6-methyladenine (6mA), 5-methylcytosine (5mC), and 4-methylcytosine (4mC). While historically most sequencing technologies could only practially detect up to two of the three types of modifications, nanopore sequencers have shown they can detect all three modifications from the same dataset at a less expensive cost than other sequencing methods. While some tools exist to analyse these data to make methylation motif calls (aka "discover the methylome"), we wrote MIJAMP (MIJAMP Is Just A MethylBED Parser) because we wanted less of an automated pipeline with no human intervention necessary (or possible, in many cases) and more of a workflow consisting of a robust set of tools developed to assist humans in analyzing genome-scale datasets.

## Installation

MIJAMP requires [MEME](https://meme-suite.org/meme/doc/download.html), [Modkit](https://github.com/nanoporetech/modkit), [Minimap2](https://github.com/lh3/minimap2), and [SAMtools](http://www.htslib.org/download/) to be present in your system's PATH, while the Python packages [Pandas](https://pypi.org/project/pandas/), [Biopython](https://pypi.org/project/biopython/), and [Xmltodict](https://pypi.org/project/xmltodict/) are also required. 

MIJAMP requires [MEME](https://meme-suite.org/meme/doc/download.html), [Modkit](https://github.com/nanoporetech/modkit), [Minimap2](https://github.com/lh3/minimap2), and [SAMtools](http://www.htslib.org/download/) to be present in your system's PATH, while the Python packages [Pandas](https://pypi.org/project/pandas/), [Biopython](https://pypi.org/project/biopython/), and [Xmltodict](https://pypi.org/project/xmltodict/) are also required. Finally, MIJAMP is only functional on AMD-based systems or containers.

To expedite installation, a dockerfile is provided to build a Docker image. First, download and decompress the MIJAMP repository.

```

$ sudo docker commit mijamp

```

Note that issues can occur when running Docker on Apple Silicon devices. MIJAMP assumes Docker is emulating an AMD version of Linux but frequently will default to emulating an ARM version of Linux on Apple Silicon. Ensure that Docker is building an AMD version of the container through Docker settings if using an ARM-based computer before running setupScript.

Note that Modkit is software exclusive to AMD processors, and thus MIJAMP can not run on ARM-based systems. When running Docker on Apple Silicon devices the default setting will emulate an ARM version of Linux. Thus, ensure that Docker is building an AMD version of the container through Docker settings if using an ARM-based computer before running setupScript.

## Quick Start Guide Using Test Data

The MIJAMP repository contains data from _Escherichia coli_ K12 MG1655 and _Picosynecococcus sp._ PCC7002 that serves as test and training data for users. Each folder contains a genome sequence and a BAM file containing 100x coverage worth of reads that have been called to detect DNA modifications, so these data are ready for preprocessing. Note that # below should be replaced with the number of threads you wish to use during preprocessing (more is definitely better).