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  UGENE Forum › General Category › Help and How-to › DE NOVO ASSEMBLY
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DE NOVO ASSEMBLY (Read 2493 times)
Dec 20th, 2020 at 7:22pm

joseluis   Offline
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Hello. I want to use CAP3 to perform a DE NOVO assembly but I am not sure if CAP3 is appropiate for NGS and paired end reads. Can somebody help me? Thank you.
 
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Reply #1 - Dec 21st, 2020 at 1:52pm

Dmitrii Sukhomlinov   Offline
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Hello,

I suggest you use "SPAdes" for De Novo Assembly.  Open "Workflow Designer", text "de novo" in the filter field of the samples tab on the left and choose "De Novo assembly PE reads". Configure steps using the wizard (you may find the information about "Trimmomatic" configuring in this video https://youtu.be/FORI6rDqT00 ), set your PE reads, and run the workflow.

The important point - the "SPAdes" tool is for Linux and macOS only, so this workflow is impossible to run on Windows.
 
Best regards,
Dmitrii Sukhomlinov,
The UGENE team.
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Reply #2 - Apr 16th, 2021 at 1:53pm

Renat   Offline
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При использовании De novo assemble PE Reads в Error list следующая ошибка: Read illumina PE Reads: Required parameter has no input urls specified: Right PE reads.

Во вкладке Dataset указываю 2 fastq файла R1_001 и R2_001.
 
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