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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Plasmid losts #261

Open bifidoman opened 3 years ago

bifidoman commented 3 years ago

Hi

I have noticed the problem of #138 quite some times in many bacteria ncluding E coli, and Clostridia. Plasmids found in Illumina assembly and detected in the lab (!), disappeared in Unicycler assemblies. Many of these plasmids carried ABR genes which should not be missed in an analysis! It is independently on the presence of short reads. It is quite annoying, especially because other assemblers (CANU, RAVEN) don't have this problem. I heard also from other scientists they have this problem.

Maybe you could check with following data https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA604100 Strain 32 and 64 have a 51-kbp plasmid that is not detected by Unicycler. The sequence is completely missing! Canu detected these plasmids.

I think this is a very severe problem. A solution must be presented and standard run setting should be able to cope with this.

For the moment, I think you should report this bug in your description. Thanks

Marc

valery-shap commented 3 years ago

Hello,

I have the same problem. Unicycler v0.4.9 lost IncI2 plasmid(60kb) with mcr in E.coli with hybrid assembly! Have you found alternative pipeline?

Valery