Scaffolding
francicco opened this issue · 3 comments
francicco commented
Hi,
Can I use MashMap to scaffold contigs from a draft genome according to the reference?
Thanks,
Francesco
cjain7 commented
Mashmap should give you mappings of contigs to reference. You will need to further process the mapping output for scaffolding application.
selasphoruskershaw commented
Hi, do you have a program you can recommend for assigning the scaffolds to chromosomes using the mashmap.out file? I need to use the mapping output from mashmap to actually find the locations of scaffolds on the chromosomes, so that I know which chromosome contains each scaffold. Thank you!
cjain7 commented
Sorry we don't have an explicit program written for this. I suggest you type a short python / R script for your application.