Question: List of plant long read genome assemblies
0
gravatar for Anand Rao
6 months ago by
Anand Rao280
United States
Anand Rao280 wrote:

Can anyone please point me to a list of plant species / genome assemblies that satisfy the following 4 criteria:

1. Long-read assembly for at least 3 accessions / ecotypes / strains for the same species (using PacBio / MinION / 3C and other technologies - agnostic of method, as long as it satisfies citerion #4 below

2. Is not Arabidopsis or it's close phylogenetic relatives (that excludes Brassica and Arabidopsis genera)

3. Prefer genome assemblies < 1GB in size, if possible. But larger ones like that of maize may be OK too, but not much larger, please

4. High contiguity, correctness and completeness, especially in regions of structural variations (so no Illumina only assemblies)

Thank you!

assembly long read plant genome • 165 views
ADD COMMENTlink written 6 months ago by Anand Rao280

Where have you looked so far?

ADD REPLYlink written 6 months ago by Friederike5.3k
2
gravatar for Anand Rao
6 months ago by
Anand Rao280
United States
Anand Rao280 wrote:

Answering my own question below in a slightly roundabout way:

1. Go to "Pubmed Assembly" at https://www.ncbi.nlm.nih.gov/assembly/organism/

2. Type in scientific name of the species of interest (plant or otherwise).

3. Filter results based on user preference, in my case, I look for assembly that is at the Assembly Level of "chromosome", and not "scaffold" or "contig".

4. Sort by date if your prefer, and of the filtered results, click on individual links to obtain further details to choose genome assemblies of interest / application to you.

Cheers!

A

ADD COMMENTlink modified 6 months ago • written 6 months ago by Anand Rao280
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