Hu Jiang
Hu Jiang
Could you provide the input config file and version?
No difference, please see the Optional part at `QUICK RUN ` section in the [main page](https://github.com/Nextomics/NextPolish). The first strategy is to do the alignment by yourself, another is to use...
As the log says `/mnt/md1/Gg_GI_polishing/Sf_polishing/Soplha_reverse_paired.fastq.g does not exist!`, it seems you have a typo, the filename ends with `gz`, not `z`.
Hi, `NextPolish` required paired-end reads should be in separate files by default, you can switch to single file input with the option `-unpaired`. For `Is it possible to create a...
Hi, depends on your input and parameters, but if you prefer to use your own alignment pipeline, it will cost less resources and be faster, [here](https://nextpolish.readthedocs.io/en/latest/QSTART.html#quick-start)
see [minimap2 manual](https://lh3.github.io/minimap2/minimap2.html) to checkout how to run minimap2, `[hifi]` is not a correct option.
what is the version of NextPolish you are using? Could you paste some seq IDs in the polished genome while not existed in the original genome?
I guess the short reads contain N, see [FAQ vi](https://github.com/Nextomics/NextPolish). BTW, pls update to the latest version.
Yes, see our paper, `Hu, Jiang, et al. "NextPolish: a fast and efficient genome polishing tool for long read assembly." Bioinformatics (Oxford, England) (2019)`
The memory is enough, NextPolish does not require much memory. I do not test wtpos-cns, for NextPolish, two round short-reads correction is enough, but if you want a more accurate...