Scaffhunter regroups several programs which principal aims are to work and visualize genetic mapping data. In addition to 2D visualization of linkage between markers, these tools can be used to order scaffolds without passing by the tedious step of genetic map construction and reconciliation between marker order in scaffold and marker order in the genetic map.
All proposed tools described here are written in python and work on linux system
To install the tools:
1- unzip the tar.gz file with the following command line : tar -xvzf
2- open the loca_programs.conf file
3- set the path to each programs required
To run fully all programs are needed:
1- blast
2- bowtie2 can be found at http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
3- bwa can be found at http://bio-bwa.sourceforge.net
4- orthodotter is provided in the bin directory with these tools
perl, python and java are required. Biopython is also required.
Two of these tools use orthodotter program provided in this archive. This program has been
developed by Jean-Marc Aury (Institut de Genomique / DSV / CEA, FRANCE) and is deposited
under CeCILL license http://www.cecill.info.
Martin G, Baurens F-C, Droc G, Rouard M, Cenci A, Kilian A, Hastie A, Doležel J, Aury J-M, Alberti A, et al. 2016. Improvement of the banana “Musa acuminata” reference sequence using NGS data and semi-automated bioinformatics methods. BMC Genomics 17:1–12 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2579-4
Guillaume Martin (CIRAD)
Licencied under CeCill-C http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html and GPLv3