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Old 04-04-2018, 02:35 AM   #1
Apodemus
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Location: Spain

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Default Paired- and Single-End Library on SoapDenovo-Trans

Hello everyone.

I'm trying to assemble a transcriptome with different assembly programs and with different k-mer sizes.
I've got both single- and paired-end reads and, to my understanding, both Velvet and Trinity can perform the assembly with this kind of libraries.

Velvet:
https://hcc-docs.unl.edu/display/HCC...aired-End+Data

Trinity: concatenating the single-end reads to the R1 of the paired reads.

Does anybody knows how to proceed with this kind of assembly in SoapDenovo-trans? There is some information about Soapdenovo2 in the same page where the Velvet information is found, but I don't know if it would be applicable for the -Trans version.

Thank you for your time.

Last edited by Apodemus; 04-04-2018 at 02:42 AM.
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