Comments (3)
Yes, see our paper, Hu, Jiang, et al. "NextPolish: a fast and efficient genome polishing tool for long read assembly." Bioinformatics (Oxford, England) (2019)
from nextpolish.
Thanks for quickly reply. Your paper mainly focus on short reads corrections and documented that two rounds is good enough, so I plan to perform one round PacBio long-reads + two round short-reads correction using wtpos-cns, and finally use NextPolish to do two round short-reads correction. Will it work?
The assembly is ~2Gb and short-reads are about 100 Gb. My severs has ~330 Gb memory, is it enough to run NextPolish?
from nextpolish.
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 assembly, you can try more iterations.
from nextpolish.
Related Issues (20)
- Empty bin directory after installation? HOT 2
- User defined alignment pipeline for short- and long-reads HOT 2
- [question] combine with medaka or not? HOT 3
- run nextplolish2.py sleep HOT 8
- Ignore the secondary alignment HOT 2
- Test run failed at map_genome: "[gzclose] buffer error" HOT 3
- Installation failure with multiple definition of 'rle_auxtab' HOT 2
- db_split failed: HOT 3
- How does NextPolish polish an assembly with long reads? HOT 1
- make[2]: *** [Makefile:30: bwa] Error 1 错误 HOT 1
- slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT HOT 1
- run fails with long read only in conda env HOT 5
- SLURM out of memory and time... HOT 1
- [main_samview] fail to read the header from "-" HOT 1
- zlib.h not found error HOT 1
- polish_genome failed HOT 1
- problem with NextPolish-CentOS6.9.tgz
- The process of polishing causes a significant decrease in genome size. HOT 8
- During the execution of samtools index, I encountered an error: "invalid option -- '@'" HOT 4
- An error message was encountered while running 00.lgs_polish/04.polish.ref.sh.work/polish_genome01
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