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genecovr

R build status

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.