NextPolish
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Nextomics
Fast and accurately polish the genome generated by long reads.
when nextpolish1.py or nextpolish2.py was used to polished my assembly，only polished.fa was get. How to stat the changes coused by nextpolish1/2.py? ‘’python ~/biosoft/nextpolish/lib/nextpolish2.py -g ${input} -l lgs.sort.bam.fofn -r ${read_type} -p...
Hi, I have tried NextPolish, and oveall I am happy with it, but I miss a bit pore possibilities to select what to polish in order to trust what is...
I encountered a problem when using nextpolish. I used a normal user to submit the job result of drmaa and reported an error. The content is: drmaa.errors.DeniedByDrmException: code 17: slurm_submit_batch_job...
**Question or Expected behavior** How long should it take for NextPolish to complete on a ~50Mb long read genome and what memory should I ask for? I submitted it at...
**Describe the bug** Hi I am trying to run NextPolish on Hifi pacbio sequences. I keep running into an unspecified error with db split. My workflow is: ls /scratch/kcl58759/Eco_pacbio_kendall/pb_css_474/cromwell-executions/pb_ccs/c7a3dc30-7f94-40de-ac16-2445f965bfad/call-export_fasta/execution/m64060_210804_174320.hifi_reads.fasta.gz >...
Hi, I am writing here to request your help to run Nextpolish. I have long read (pacbio sequel 1) and illumina reads, and I wanted to polish the assembly. After...
Hi all. I'm trying to polish an assembly from Flye for nanopore reads. However, I cannot make the command work as I receive errors that I cannot determine the source,...
I've loaded NextPolish onto a virtual Ubuntu 20.04.2 LTS system and the install seems to have completed without issue, but when I run the test data, I've encountered a traceback...
**Question or Expected behavior** I have a reference genome obtained after CANU assembly, purge_dups and long reads polishing with arrow. I'd like to polish with short reads using Next_polish. Should...
From last few days i am trying to use NextPolish. When i meet the trouble for the first time i went to user guideline and found that the author has...
