Quast Evaluator

Depends on Quast version 3.2

Install

Pandoc (version > 1.17) must be installed

1.Clone this repository with git clone https://github.com/pbelmann/quast-evaluator.git

2.Change working directory: cd quast-evaluator

3.Run R -e 'install.packages("packrat" , repos="http://cran.us.r-project.org"); packrat::restore()'

User Guide

Quast Evaluator has two modes:

'new' Mode

This mode lets you collect quast results from different quast output directories.

Run

Rscript quast_evaluator_cli.r new /path/to/assemblers.tsv /path/to/info.tsv -o /path/to/output/directory

where assemblers.tsv and info.tsv must have the following columns:

assemblers.tsv:

name	assembler       path	group
assembler1	jolly_euclid_1  /home/belmann/projects/quast-evaluator/tests/testthat/data/assembler1	1
assembler2	angry_newton_2  /home/belmann/projects/quast-evaluator/tests/testthat/data/assembler2	2

where

/home/belmann/projects/quast-evaluator/tests/testthat/data/assembler1 must contain the directories runs_per_reference and combined_reference
name is the assembler name that will be shown in the plots
assembler is the name of the assembler provided to metaquast.
info.tsv:

id              path	        group	length	mapping	
1030752.gt1kb   1030752.gt1kb   strain	1200	43000
1030755.gt1kb   1030755.gt1kb   strain	2300	89999
1030836.gt1kb   1030836.gt1kb   evolved	4500	76666
1030878.gt1kb   1030878.gt1kb   evolved	8999	50000

where

path is a directory inside the runs_per_reference directory.
id is a uniq identifier
group is an identfier which groups different references
length is the length of the reference
mapping how many reads are mapped to the specific reference

'reuse' Mode

This mode lets you reuse tsv files produced by the 'new' mode.

Run

Rscript quast_evaluator_cli.r reuse /path/to/combined_ref_data.tsv /path/to/ref_data.tsv -o /path/to/output/directory

where combined_ref_data.tsv and ref_data.tsv have the columns stated in these example files: tests/testthat/data/ref_data.tsv and tests/testthat/data/combined_ref_data.tsv

Further Parameters:

'-c /path/to/plot.conf' This file allows you to define min and max for each plot individually. The here for an example.

Example

See tests

Developer Guide

You can run tests with

R -e 'devtools::test()'

Please use this if you want to propose a Pull Request.

pbelmann / quast-evaluator