Question

Mapping scaffolds to chromosomes

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6.3 years ago

hpapoli ▴ 150

Hello,

I have a list of species with scaffold level assemblies. There is one species in the clade with chromosome level assembly. How can I approximately map scaffolds to chromosomes for my list of species?

I know about LASTZ, one way would be to align each species to the one with chromosome level assembly with LASTZ. I was wondering if there are other methods for this?

Thanks!

lastz assembly • 2.2k views

ADD COMMENT • link updated 6.3 years ago by FGV ▴ 170 • written 6.3 years ago by hpapoli ▴ 150

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A recent review on long-range sequencing has a list of scaffolding programs you can use in Table 2.

ADD REPLY • link 6.3 years ago by GenoMax 147k

score 1 · Answer 1 · 2018-08-01

How big are the genomes? If small you can try MAUVE or MUGSY...

I needed to align some bird genomes a while ago, and in the end had to use MULTIZ. It is a bit of a pain to use but it the end it worked.

You might also be interested in looking into minimap2 or cactus. I've never used any of them but it seems they might do the job...