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JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
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PiRATE pipeline. #38

Closed Lukanyo12 closed 3 years ago

Lukanyo12 commented 3 years ago

Hello, can we use PiRATE for retrieval and annotation of transposable elements in fungal genomes, specifically Basidiomycota?

JBerthelier commented 3 years ago

Dear Lukanyo,

Yes, PiRATE can be use with all organisms! It will only be limited by your computational force, because at now it only work on a local computer. If your organisms has a relative small genome (less than 500 Mb) it should be fine with a good computer. How long is the genome assembly? What is your computational configuration?

As example: I am using 10 cores and 28 Mb of memory for the Virtual Machine of PiRATE installed on my local computer.

Best

Jeremy

Lukanyo12 commented 3 years ago

Thank you for your reply! I was worried. My genome assemblies ranges from 60 to 90 Mb.Well my CPU has 2 cores on window 10.

On Fri, Jul 17, 2020 at 8:57 AM Jérémy Berthelier notifications@github.com wrote:

Dear Lukanyo,

Yes, PiRATE can be use for all organisms! It will only be limited by your computational force, because at now it only work on a local computer. If your organisms has a relative small genome (less than 500 Mb) it should be fine with a good computer. How long is the genome assembly? What is your computational configuration?

As example: I am using 10 cores and 28 Mb of memory for the Virtual Machine of PiRATE installed on my local computer.

Best

Jeremy

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/JBerthelier/PiRATE/issues/38#issuecomment-659905673, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQJ3NWL33NTHHTCXQF4YPIDR37Y55ANCNFSM4O47GKPQ .

JBerthelier commented 3 years ago

Dear Lukanyo,

No problem! According that your are going to analyse a relative small genome size, the PiraTE should be able to run on your local computer. But for sure it gonna take a time for the tool to finish. The big one tools (TEdenovo, PASTEC and TEannot) will probably take longer time than other tools to finish.

Best regards,

Jeremy

Lukanyo12 commented 3 years ago

Any idea of how can I overcome that and make it fast maybe?