UGENE Forum - How to open assembled genome in ugene?

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How to open assembled genome in ugene? (Read 2345 times)

Dec 14^th, 2019 at 3:46am

JoeL Offline
YaBB Newbies

Posts: 1

Hi @ll!

I'm a first-time ugene user and looked through tutorials, manuals and podcasts but I cannot find a solution. Hence, I hope that you can help me out here:

I would like to use ugene to open the following assembled genome ncbi.nlm.nih.gov/assembly/GCA_004329575.1/ but I always get the error message "genome too big, use NGS methods under "Tools". However, I cannot find a way to import this genome to ugene. Could anyone here help out by telling me how to do it?

Thanks!
Joe

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Reply #1 - Dec 16^th, 2019 at 5:46pm

Olga Golosova Offline
YaBB Administrator

Posts: 338

Hi Joe.

How do you download the data (there are different options)?

For example, if you download the data as the "Genomic FASTA" file type from the "GenBank" source database, the downloaded archive file "genome_assemblier.tar" contains "GCA_004329575.1_ASM432957v1_genomic.fna.gz" file that contains 7999881 scaffold sequences. You may unpack this file as well and open it in a text editor.

It doesn't make much sense to view all these ~800000 sequences at once, although it is possible to "merge sequence into a single sequence show in sequence viewer", when opening the file.

So, the main question is what do need to do with this data? Depending on your needs I may give you further recommendations.

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