Some question about pacbio hifi data polish

[xiaobaiymq]

Question or Expected behavior A clear and concise description of your question or what you expected to happen.

Question or Expected behavior I first use hifiasm to get the haplotype assembly and then use Nextpolish to polish, but I found a change after polish. At primary assembly,it is not have N

Mismatches  
# N's   0
# N's per 100 kbp   0

but in polish assembly，which have a lot of Mismatches
Mismatches  
# N's   40
# N's per 100 kbp   0.01

I don't kown this is normal

thanks

Operating system LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.5.1804 (Core) Release: 7.5.1804 Codename: Core

GCC gcc 版本 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC)

Python Python 3.8.5

NextPolish nextPolish v1.3.0

Additional context (Optional) Add any other context about the problem here.

[moold]

Could you paste your config file to here?

[xiaobaiymq]

This is my run.cfg [General] job_type = local ## local, sge, pbs... (default: sge) job_prefix = nextPolish1 task = best rewrite = no rerun = 3 parallel_jobs = 2 multithread_jobs = 3 genome =xx.asm.hic.hap1.p_ctg.fa genome_size = auto workdir = ./rundir polish_options = -p {multithread_jobs}

[sgs_option] sgs_fofn = ./sgs.fofn sgs_options = -max_depth 100 -bwa

[lgs_option] lgs_fofn = ./lgs.fofn lgs_options = -min_read_len 5k -max_depth 100 lgs_minimap2_options = -x map-pb

2021年11月26日 16:40，Hu Jiang @.***> 写道：

Could you paste your config file to here?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextPolish/issues/85#issuecomment-979788401, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATGFUSRSO3LJWTZNZWBH33LUN5BWXANCNFSM5I2BE5XQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[moold]

see here

[xiaobaiymq]

I get, Is it necessary to remove N but how to remove N, and how to remove N if necessary

2021年11月26日 22:34，Hu Jiang @.***> 写道：

see here https://nextpolish.readthedocs.io/en/latest/FAQ.html#why-does-the-contig-n50-of-polished-genome-become-shorter-or-why-does-the-polished-genome-contains-some-extra-n — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextPolish/issues/85#issuecomment-980023506, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATGFUSU4RKHIKPJCYO7MUXTUN6LI5ANCNFSM5I2BE5XQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

[moold]

1. Does the input sgs.fofn contains N?
2. Is the input lgs_fofn hifi data? If yes, you should use hifi_option, see here.
3. If the assembly was assembled from HiFiasm, there is not much need to do polishing, because HiFiasm already include an error-correction step.

[xiaobaiymq]

Thank you very much ,I get you

2021年11月29日 13:44，Hu Jiang @.***> 写道：

Does the input sgs.fofn contains N? Is the input lgs_fofn hifi data? If yes, you should use hifi_option, see here https://nextpolish.readthedocs.io/en/latest/TUTORIAL.html#polishing-using-short-reads-and-hifi-reads. If the assembly was assembled from HiFiasm, there is not much need to do polishing, because HiFiasm already include an error-correction step. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Nextomics/NextPolish/issues/85#issuecomment-981309738, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATGFUSVDOOSROEALV6BI3QTUOMHLXANCNFSM5I2BE5XQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.