genecovr

Perform gene body coverage analyses in R to evaluate genome assembly quality.

Installation

You can install the released version of genecovr from NBIS GitHub with:

# install.packages("devtools")
devtools::install_github("NBISweden/genecovr")

Quick usage

There is a helper script for generating basic plots located in PACKAGE_DIR/bin/genecovr. Create a data input csv-delimited file with columns

1. data label
2. mapping file (supported formats: psl)
3. assembly file (fasta or fasta index)
4. transcript file (fasta or fasta index)

Columns 3 and 4 can be set to missing value (NA) in which case sequence sizes will be inferred from the alignment files. Then run the script to generate plots:

PACKAGE_DIR/bin/genecovr indata.csv

Vignette

Alternatively, import the library as usual in an R script and use the package functions. See the vignette for a minimum working example.