genecovr

genecovr is an R package that provides plotting functions that summarize gene transcript to genome alignments. The main purpose is to assess the effect of polishing and scaffolding operations has on the quality of a genome assembly. The gene transcript set is a large sequence set consisting of assembled transcripts from RNA-seq data generated in relation to a genome assembly project. Therefore, genecovr serves as a complement to software such as BUSCO, which evaluates genome assembly quality using a smaller set of well-defined single-copy orthologs.

Installation

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

# If necessary, uncomment to install devtools
# install.packages("devtools")
devtools::install_github("NBISweden/genecovr")

Usage

genecovr script quick start

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

data label
mapping file (supported formats: psl)
assembly file (fasta or fasta index)
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

Example

There are example files located in PACKAGE_DIR/inst/extdata consisting of two psl alignment files containing gmap alignments and fasta indices for the transcript sequences and two for different assembly versions:

nonpolished.fai - fasta index for raw assembly
polished.fai - fasta index for polished assembly
transcripts.fai - fasta index for transcript sequences
transcripts2nonpolished.psl - gmap alignments, transcripts to raw assembly
transcripts2polished.psl - gmap alignments, transcripts to polished assembly

Using these files and the labels non and pol for the different assemblies, a genecovr input file (called e.g., assemblies.csv) would look as follows:

nonpol,transcripts2nonpolished.psl,nonpolished.fai,transcripts.fai
pol,transcripts2polished.psl,polished.fai,transcripts.fai

and the command to run would be:

genecovr assemblies.csv

genecovr options

To list genecovr script options, type ’genecovr -h`:

usage: genecovr [-h] [-v] [-p number]
                             [-d OUTPUT_DIRECTORY] [--height HEIGHT]
                             [--width WIDTH]
                             csvfile

positional arguments:
  csvfile               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)

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         print extra output
  -p number, --cpus number
                        number of cpus [default 1]
  -d OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
                        output directory
  --height HEIGHT       figure height in inches [default 6.0]
  --width WIDTH         figure width in inches [default 6.0]

R package vignette

Alternatively, import the library in an R script and use the package functions. See Get started or run vignette("genecovr") for a minimum working example.