I’m working with high polymorphic target genes and I need as much accuracy as possible to be able to create my own references.
If I want to use 1D2 reads, will be Albacore the only software available? I will have Illumina short reads as well to map against the nanopore’s in the pre-assembly step for further error correction.
Any other tips to increase the accuracy of base assignement using MinION?
Thanks
You can read those few pages online. https://github.com/rrwick/Basecalling-comparison ... Whether you are student, or a researcher, this might be of some interest to you. Not as an answer to your question, but as a source of ideas to consider.
Good luck.
You can read those few pages online. https://github.com/rrwick/Basecalling-comparison ... Whether you are student, or a researcher, this might be of some interest to you. Not as an answer to your question, but as a source of ideas to consider.
Good luck.
rrwick's github repo from Mohammed's reply would also have been my first suggestion.
The repo clearly indicates the improvements that are possible from *assembling*, i.e., creating a consensus sequence from the raw reads.
However, a "simple" assembly will only bring you so far - for now.
This means that you can actually further improve the overall accuracy by *polishing* the assembly, rather than polishing the reads *prior* to assembly.
AFAIK, there are two main ways of polishing: Using the raw reads in combination with, e.g., nanopolish, and/or using short reads, e.g., Illumina-based, with Quiver/Arrow/etc.
For an E. coli genome, we found the nanopolish step (incl. homopolymer correction and methylation-aware option) to substantially reduce the number of SNPs and, thereby, to substantially reduce the number of missed/wrongly called genes due to frameshifts (s. https://twitter.com/davidacoil/status/968917784905199616 and https://twitter.com/claczny/status/973888479359840256).
Moreover, and probably most importantly with respect to your question, running a round of polishing was able to cancel out the majority of differences between the basecallers.
In summary, it depends on what your goal is, but if assembly + polishing is an option, the basecaller has a minor impact on the sequence identity.
Best,
Cedric
this link is useful
https://github.com/rrwick/Basecalling-comparison
regards
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