What would be alternative options for using Canu for the whole genome assembling? My basecalling output format is fastq files, and I am planning to use it as input files for Canu. I know that using Canu might be challenging, so I'm exploring alternative options, just in case. . Thank you very much, I would appreciate any suggestions.
Hello Alina,
What plataform did you use to sequence your data PacBio or Nanopore?
Hello Alina
Are you doing polising with illumina reads after de assembly? If so, I will MaSurCa or the ONT pipeline from Nanopore. I am leaving you the links here. Also, try both is not that one pipeline is better than other it really depends on what you are sequencing. I always recomend trying at leat two assemblers.
Cheers
Silvia
https://github.com/nanoporetech/ont-assembly-polish
https://github.com/alekseyzimin/masurca
Silvia, thank you very much for the links! I haven't done polishing (I'm still learning the whole process) but I'll keep these pipelines in mind. Thanks again!
We used wtdbg2 in several projects, recently. It is much faster than canu and gave good results. We have used it with MinION and PacBio (separately), and in combination of PacBio and Illumina.
Thank you, Katharina, that's helpful! We did sequencing with MinION only so far.
Hi Alina, I've been working on PacBio only (60-80x coverage) reference assembly of a non-model species (Coregonus whitefish - with a genome size of ~3Gb) and have tried to assemble using Falcon, Canu and wtdbg2. I'm not sure of the complexity/size of the genome you are assembling but if you are curious how different assemblers fare with a relatively big/complex genome I have attached a comparison of the summary statistics (and BUSCOs) from the output of each. I also used purge_haplotigs (https://bitbucket.org/mroachawri/purge_haplotigs) after assembly to identify and remove haplotigs (from heterozygous regions) and the statistics after this step are also included. Although Canu and wtdbg2 assemblies look very similar wtdbg2 is orders of magnitude quicker than Canu so it's definitely a great option if you are restricted with time. Hope this helps you!
Rishi, thanks so much for such detailed information!! I am on the exploring stage so far, and I have to learn a lot, of course, but this statistical comparison is very helpful, and yes, it looks like wtdbg2 is a great option.Thank you, again!
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Methods
- Cloning