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marbl / MashMap

A fast approximate aligner for long DNA sequences
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Scaffolding #26

Open francicco opened 4 years ago

francicco commented 4 years ago

Hi,

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

Thanks, Francesco

cjain7 commented 4 years ago

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

selasphoruskershaw commented 4 years ago

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 4 years ago

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