README.md

In celiason/genomeR: Tools for the analysis and assembly of genomic data in R

Genome analysis in R

This is the development version of the R package genomeR

Intro

I wrote these functions to streamline comparative genomics projects I've been working on. Use at your own risk, as this package is currently under development.

You can install the package using the devtools R package:

install.packages("devtools")
devtools::install_github("celiason/genomeR")
library(genomeR)

Tips for using the scripts

To align reads in file "myreads.fastq.gz" to reference "myref.fa" run the following:

alignReads(ref="myref.fa", reads="myreads.fastq", cores=48, ram=150, suffix="run1")

Note: the directory structure should be such that there is a folder called "genomes" with 6-letter species abbreviations as subfolders (e.g., "anaPla" for the mallard, Anas platyrhynchos). The code above will run a QC analysis using the fastp program (must be installed) and output a sorted BAM alignment file with the following naming convention: READS-to-REF.bam (e.g., "anaPla-to-galGal.bam" for mallard aligned to the chicken genome Gallus gallus).

Author

Chad M. Eliason Field Museum, Chicago IL

celiason/genomeR documentation built on Sept. 9, 2024, 1:11 p.m.