Scaffremodler regroup a severals programs which principal aims is to detect use paired reads to
link different genomic regions. These main programs are accompanied with a severals others
programs that can be used in complement to improve scaffold assemblies or to detect large
structural variations between a reference sequence and a re-sequenced genome.
All proposed tools described here are written in python and work on linux system To install the tools: 1- unzip the folder 2- go to the bin directory and open the loca_programs.conf file 3- set the path to each programs required (listed below) To run fully all programs are needed: 1- bowtie can be found at http://bowtie-bio.sourceforge.net/index.shtml 2- bowtie2 can be found at http://bowtie-bio.sourceforge.net/bowtie2/index.shtml 3- SortSam.jar, MarkDuplicates.jar and FilterSamReads.jar belong to Picard Tools and can be found at http://broadinstitute.github.io/picard/ 4- bwa can be found at http://bio-bwa.sourceforge.net 5- samtools can be found at http://www.htslib.org 6- circos-0.67-7 is required and can be found at http://circos.ca/software/download/circos/ perl, python and java are required. Biopython is also required. 7- bamgrepreads can be found at https://code.google.com/p/variationtoolkit/wiki/BamGrepReads
Please cite either:
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, Françoise Carreel, Olivier Coriton, Catherine Hervouet, Céline Cardi, Paco Derouault, Danièle Roques, Frédéric Salmon, Mathieu Rouard, Julie Sardos, Karine Labadie, Franc-Christophe Baurens, Angélique D’Hont. 2017. Evolution of the banana genome (Musa acuminata) is impacted by large chromosomal translocations. Molecular Biology and Evolution https://academic.oup.com/mbe/article/34/9/2140/3852084
Guillaume Martin (CIRAD)
Licencied under GPLv3