README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd with devtools::build_readme(). Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# genecovr

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

## Installation

You can install the released version of genecovr from [NBIS
GitHub](https://github.com/nbis) with:

``` r
# 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:

``` shell
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.