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dzerbino / velvet

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
https://europepmc.org/article/pmc/2336801
GNU General Public License v2.0
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Contig length #51

Closed azrasid closed 3 years ago

azrasid commented 4 years ago

Hi, I am using velvet to de novo assemble a gene. I got contigs and scaffolds. Is there any way to improve the quality of contigs- a good length of contig.

Your suggestions will be highly appreciated.

Thanks, Azra

dzerbino commented 4 years ago

Hello Azra,

There are a number of ways. In short it really depends on the data available: do you have paired end reads, long reads etc?

The setting of parameters, in particular the hash length and coverage cutoff can also be adjusted to improve results. More information here: https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471250953.bi1105s31?casa_token=oFVJez9KtigAAAAA%3Af6Fi2dJ6rBASq8xikrW7wUjhYj85BEUlLOsVqon3CgZ_ifMcoXU63pCsn-A9XQW74-3WRhXrhh3cKkvV

Hope this helps,

Daniel

azrasid commented 3 years ago

Yes it is helpful. Thanks and best wishes.