List of plant long read genome assemblies
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4.9 years ago
Anand Rao ▴ 630

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!

plant genome long read Assembly • 818 views
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Where have you looked so far?

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4.9 years ago
Anand Rao ▴ 630

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

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