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ruanjue / wtdbg2

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
GNU General Public License v3.0
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Genome Size Parameter vs. Output consensus #176

Closed agos316 closed 4 years ago

agos316 commented 4 years ago

Hello, I am new to de novo assembly and this program is the only one I could use so far that generates a consensus sequence with the resources I have. My question is about the genome size parameter. I put 13.7k for the genome size and the output sequence was ~40k. Is there a reason behind this ? I am using Nanopore reads.

Best

Marc

ruanjue commented 4 years ago

Genome size is used to choose parameters, e.g. -k, -S. Combined with coverage cutoff -X, another use is to filter input reads. It have no direct impact on the final assembly size. In your case, please map the reads on assembled contigs to get more information.

agos316 commented 4 years ago

Thank you for your quick response, I will try this today !