Difference b/w primary and alternate genome assembly ?

Question

[sunnykevin97]

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!

Answer 1

[GenoMax]

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.

[sunnykevin97]

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!

[GenoMax]

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

[pinn]

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

For phylogenetics studies which assembly is prefered ?

[sunnykevin97]

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.