Wrapper for 'minimap2'

Wrapper for 'Minimap2'. 'Minimap2' is a very valuable long read aligner for the Pacbio and Oxford Nanopore Technologies sequencing platforms. 'minimapR' is an R wrapper for 'minimap2' which was developed by Heng Li . *SPECIAL NOTES 1. Examples can only be run from 'GitHub' installation. 2. 'conda' or 'mamba' must be used to install 'minimapR' on your system. 3. For Windows users, 'minimap2' and 'samtools' can be installed via MSYS2, instructions are provided when 'minimap2_installation()' is run. Li, Heng (2018) "Minimap2: pairwise alignment for nucleotide sequences".

Installation

git clone https://github.com/jake-bioinfo/minimapR.git

R CMD INSTALL minimapR

System Requirements

This package requires Git to be installed on your system. Git is used for cloning repositories.

Installing Git

• Windows: Download and install Git from gitforwindows.org.
• macOS: Install Git via Homebrew with brew install git.
• Linux: Install Git using the package manager, e.g., sudo apt-get install git for Debian-based systems.

Ensure that Git is included in your system PATH so that it can be accessed from the command line.

This package is based on the work of Heng Li. It is a wrapper for a package written by him 'minimap2' http://liheng.org/ https://github.com/lh3/minimap2

Citations

Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100. doi:10.1093/bioinformatics/bty191

Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. doi:10.1093/bioinformatics/btab705