Scaffolding

[francicco]

Hi,

Can I use MashMap to scaffold contigs from a draft genome according to the reference?

Thanks,
Francesco

[cjain7]

Mashmap should give you mappings of contigs to reference. You will need to further process the mapping output for scaffolding application.

[selasphoruskershaw]

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]

Sorry we don't have an explicit program written for this. I suggest you type a short python / R script for your application.