number of Illumina reads for transcriptome assembly

[glopatriello]

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Hi there!

I am performing a de novo transcriptome assembly of a non model organism. To do that, we have sequenced RNA with ONT and Illumina and we are going to build the transcriptome using the hybrid approach.

I was wondering if in the hybrid approach rnaSPAdes requires a certain number of sequenced Illumina reads(for istance 200 milion of fragments) or the more I sequence the better the results will be.

Best regards,
Giulia

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[andrewprzh]

Dear Giulia

There is no certain limit for number of short reads you provide. However, low-covered datasets (let's say below 10-15 M reads may give sub-optimal results). Very high coverage datasets, on the other hand, may take a long time to assemble. From our experience 50-200M reads is a good balance for typical eukaryotic transcriptome.

Best
Andrey