What is Scarpa?

Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. Scarpa 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 Scarpa. Click here for the supplementary material.


To install Scarpa:

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


On a GNU environment run the command:

tar -xzvf scarpa-0.241.tar.gz

This will unzip and extract the files to a directory named "scarpa-0.241". Change your directory to "scarpa-0.241" and follow the instructions given in SCARPA.README. Please note that Scarpa is mainly tested in 64-bit Linux-based environments. You may install Scarpa on a 32-bit environment however this is not recommended due to memory limitations.

Changes from previous versions:

--- from version 0.23 ---
- minor changes

--- from version 0.22 ---
- a bug in library size calibration is fixed (when library deviation is too high or too low, the adjustment wasn't reliable)

--- from version 0.21 ---
- a bug in library adjustment is fixed (concerning datasets where the largest contig size equals N50)

--- from version 0.2 ---
- an issue related to parsing of SAM files is fixed
- documentation is revised

System requirements:

The Scarpa package requires the following to install and run successfully. Listed in parenthesis are the versions used to test the current Scarpa 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.