Question

Difference b/w primary and alternate genome assembly ?

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4.3 years ago

sunnykevin97 ▴ 980

HI

Can some one give better explanation of primary and alternate genome assembly ?

The organism I'm working has only "primary assembly" can I use this assembly for my data analysis work?

Need suggestions!

genome Assembly • 1.5k views

ADD COMMENT • link updated 4.3 years ago by GenoMax 141k • written 4.3 years ago by sunnykevin97 ▴ 980

score 5 · Accepted Answer · 2020-01-02

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4.3 years ago

GenoMax 141k

NCBI's assembly model is described on this page. If a RefSeq assembly is available for your organism then you should use that for your (unspecified above) analysis.

ADD COMMENT • link 4.3 years ago by GenoMax 141k

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The primary assembly contains only 26 Chromosomes (25 + mtDNA). The unplaced scaffolds (23) information was missing in the genome assembly. Can I use this as a ref genome for mapping transcriptome ? suggestions!

ADD REPLY • link 4.3 years ago by sunnykevin97 ▴ 980

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Unless you are specifically interested in alternate haplotypes/unplaced scaffolds you can use the primary assembly.

ADD REPLY • link 4.3 years ago by GenoMax 141k

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Does the alternate genome assembly has more information than the primary assembly.

For phylogenetics studies which assembly is prefered ?

ADD REPLY • link 22 months ago by pinn ▴ 210

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It's up to YOU, It better go for Alternate genome assembly, more genome information.

Especially for Phylogenetic studies, genome coverage I'd be very low (~9-50X). You can give it a try.

ADD REPLY • link 22 months ago by sunnykevin97 ▴ 980