What is Encore?

Encore is a sequencing error correction tool that is designed for highly polymorphic genome sequencing projects. It can be used as a preprocessing tool for de novo assembly or as a read correction tool for any other purpose. It supports multiple NGS platforms and is suitable for low-polymorphism datasets as well as datasets with high SNP and micro-indel rates. Encore is available free of charge for academic and commercial use under the GNU General Public License (GPL).

See the user manual or the paper for more information about Encore.


To install Encore:

Click the link below to download the latest version of Encore.


On a GNU environment run the command:

tar -xzvf encore-1.31.tar.gz

This will unzip and extract the files to a directory named "encore-1.31". Change your directory to "encore-1.31" and follow the instructions given in ENCORE.README. Please note that Encore is mainly tested in 64-bit Linux-based environments. You may install Encore on a 32-bit environment however this is not recommended due to memory limitations.

Changes from previous versions:

--- from version 1.21 ---
- a memory bug regarding datasets with several hundred million reads is fixed

--- from version 1.2 ---
- documentation is revised

System requirements:

The Encore package requires the following to install and run successfully. Listed in parenthesis are the versions used to test the current Encore package. These utilities must be accessible via the system path:

make (GNU make 3.81)
g++ (GNU gcc 4.4.6)
bash (GNU bash 3.2.25)
perl (v5.8.8)

Older versions:

We will make the previous versions available for a limited time however we strongly encourage users to download the latest version.