gt Scaffolder is a free scaffolding software and was developed as a student project (in the research group for genome informatics) at the Center for Bioinformatics, Hamburg. It is based on the GenomeTools-Library and is intended to be used in a de novo assembly pipeline with Readjoiner (an assembly software available in GenomeTools).
gt Scaffolder tries to solve the Contig Scaffolding Problem in the style of SGA Scaffold by using a scaffold graph and thus achieves competitive results at a low time and memory footprint. It is also fully compatible with the SGA assembly pipeline.
Please note that gt Scaffolder is not ready for production yet. The finished software will be included in GenomeTools. As of now it can successfully compute scaffolds using SGA-compatible input files. Both the interface to Readjoiner as well as the possibility to reconstruct the target sequence are still immature and need further development.
gt Scaffolder should run on every POSIX compliant UNIX system, for example, Linux, Mac OS X, and OpenBSD. This will build gt Scaffolder both as a stand-alone binary and as a gt Tool.
# Clone gt Scaffolder
git clone https://github.com/dorleosterode/gt-scaffold.git
# Clone and switch to gt_scaffolder branch of our GenomeTools fork
git clone https://github.com/dorleosterode/genometools.git
cd genometools
git checkout gt_scaffolder
# Set GTDIR
GTDIR=$(pwd)
# Simlink gt Scaffolder files into GenomeTools
cd src/match/
ln -s ../../../gt-scaffold/src/gt*.c .
ln -s ../../../gt-scaffold/src/gt*.h .
cd -
# Build GenomeTools with gt scaffolder as a tool
make -j4 cairo=no pango=no
cd ..
# Build gt Scaffolder stand-alone binary
cd gt-scaffold/src
make