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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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Simultaneous assembly of two similar genomes #228

Closed lamenace91 closed 3 years ago

lamenace91 commented 3 years ago

Hello,

The purpose of our project is to assemble the genome of a parasitic unicellular eukaryotic by using ONT reads.

Some preliminary analyses based on short reads indicate that our DNA samples and sequence libraries actually include two related genomes/species with similar length (approx 10Mb) and 10-15% of genomic divergence. Moreover, we know that one species is more prevalent than the other one into the samples (approx 2/3 versus 1/3 of DNA).

Our first assemblies with wtdbg2 and default settings produced a genome of 11Mb.This genome is similar to the most frequent genome into the samples.

We are wondering if there is a way to get the assembly of both genomes and particularly for the less frequent species?

ruanjue commented 3 years ago

wtdbg2 tends to collapse similar genomic sequences. Maybe you can choose CANU, Flye to try. If want to have a test on wtdbg2, please try to increase -s and -l, which might be useful in distinguishing similar seuqences.

lamenace91 commented 3 years ago

Thanks a lot for the quick answer. I will have a try at these parameters. My genomes are small so I should be able to explore different set of values (not so long to run an assembly) to see if I can get a better result.

lamenace91 commented 3 years ago

Hello, I wanted to let you know that I ran different assemblies with "-s" varying from 0.05 to 0.5 (steps: 0.05) and "-l" varying from 200 to 400 (steps: 50) and I obtained an assembly with two genomes with the expected size and the expected divergence. A value of "-s" around 0.3 seems to be the key parameter/value in my case since I got similar assemblies with the different values tested for "-l". I still have some work before publication but it's on the good way ... :-) Thanks again for your help.

ruanjue commented 3 years ago

Thanks for sharing the experience.