Update paper.md / modified summary

Publication/paper.md

@@ -26,7 +26,7 @@ bibliography: paper.bib
 
 # Summary
 
-Dot plots are widely used to quickly compare sequence sets. They provide a syntetic overview, highlighting alignment errors. Much tools have been developed to generate genomic alignment dot plots, but these tools often take time and require many steps before obtaining our dot-plot. The use of these different tools can be simplified through the use of pipelines.
+With the availability of cheap long read sequences and efficient software packages, novel genome assemblies are made available frequently. It is not rare to produce multiple references of the same or closely related species in a project. These assemblies being produced independently raw assembly file include chromosomes or scaffolds in random order and with random sequence names. Scientists usually decide to organize assembly files in the same way and therefore have to rename, orient and order the sequences in the files as a reference. The genomorder pipeline has been developped to automatize these tasks. It uses a reference assembly and reorganizes and renames sequences found in other assembly files according to the reference. If the reference file is in chromosomes and some of the other assemblies are in scaffolds it can organize scaffold as chromosomes. After producing several novel related assemblies scientists are also interest in visually comparing them. Therefore genomorder produces per chromosome d-genies archive output files for a given list of chromosome names. These files can be uploaded to http://dgenies.toulouse.inra.fr which will render the dot plots enabling to visualy compare all corresponding chromosomes from the produced assemblies.
 
 # Statement of need