/Red

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.

Primary LanguageC++

Red

Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.

Requirement: GNU gcc8.2 or higher. Please change the name (CXX) of the compiler in the Makefile or pass the CXX to make as shown below.

Compiling the source code

The following command makes the required directories:

make bin

The following command makes the binary that is located under the ``bin'' directory:

make

Alternatively:

make CXX=g++-8

To find the binary:

cd ../bin

Please cite the following paper:

Girgis, H.Z. (2015) Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics, 16, 227.

Ensembl fork

This fork adds option -frm 3 to produce 1-based inclusive coordinates for Ensembl, as needed in https://github.com/Ensembl/plant-scripts