User defined alignment pipeline for short- and long-reads

[Rensco Hogers]

Question or Expected behavior
I am currently running into an issue when running NextPolish using short- and long-reads. It seems that the process is killed during samtools sort, seemingly due to too little memory when running through SLURM. I would like to solve this by running my own alignment pipeline, but there are only examples for running your pipeline for short-reads or long-reads, not both. Is it as simple as combining both in one script, or do you have a better suggestion?

Operating system
Which operating system and version are you using?
Ubuntu 20.04 LTS

GCC
What version of GCC are you using?
11.2.0

Python
What version of Python are you using?
3.10.8

NextPolish
What version of NextPolish are you using?
1.4.1

[Hu Jiang]

You can try to polish the genome twice using long-reads, and then polish the genome (the polishing result with long-reads) twice using short-reads. This is the same as the default strategy used by NextPolish.

[Rensco Hogers]

Sorry for the late reply, but I have created my own pipeline based on your suggestions and the information on GitHub and it works! Thanks for the help.