Hello every one Is there an assembler (using HiFi reads as input) with web-based graphical user to do a denovo assembly?
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walid.cbs •
1 answer
I would recommend one of the ones below as they are assemblers specifically designed with PacBio HiFi reads in mind. Because of the high accuracy of HiFi reads (>Q20) you also don't need to add any Illumina data for polishing.
Running these from a GUI is likely not possible but the HiCanu and Falcon ones can definitely be done via bioconda which may be your best bet. I am not as familiar with the hifiasm one as it is relatively new but have heard good things about it.
HiCanu (Blog Description) https://genome.cshlp.org/content/early/2020/08/14/gr.263566.120
hifiasm (Blog Discription) https://github.com/chhylp123/hifiasm
Falcon / Falcon-Unzip https://github.com/PacificBiosciences/pb-assembly
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If you are looking for a free software program that is web-based and also has a GUI then I doubt one exists.
If you need a graphical user interface then using SMRT Analysis provided by PacBio is likely your best bet. Check on the compute hardware requirements.
thanks for your reply Genomax Good idea but I need an universal assemblere that accepts PacBio and illuminates reads