Issues

• Polishing ONT with HiFi vs Illumina

  Nextomics/NextPolish#146 · Filter by author Tsvanorden opened on Oct 8, 2026

• samtools sort: failed to create "lgs.part001.sort.bam": Stale file handle

  Nextomics/NextPolish#144 · Filter by author Peterhhb opened on Aug 7, 2025
  7

• polish for scaffod.fa(contain Ns)

  Nextomics/NextPolish#139 · Filter by author DayTimeMouse opened on Oct 2, 2024
  1

• NextPolish for metagenome?

  Nextomics/NextPolish#138 · Filter by author 123chenshixin opened on Sep 14, 2024
  1

• After I run nextPolish run.cfg, the NextPolish vanished and generate a copy

  Nextomics/NextPolish#135 · Filter by author SoSongzhi opened on Aug 28, 2024
  2

• The telemore sequences were removed after Nextpolish

  Nextomics/NextPolish#134 · Filter by author YouxinZhao opened on Jul 28, 2024
  1

• An error message was encountered while running 00.lgs_polish/04.polish.ref.sh.work/polish_genome01

  Nextomics/NextPolish#132 · Filter by author jiuyaojiaonini opened on Apr 23, 2024

• The process of polishing causes a significant decrease in genome size.

  Nextomics/NextPolish#130 · Filter by author xujialupaoli opened on Apr 11, 2024
  11

• problem with NextPolish-CentOS6.9.tgz

  Nextomics/NextPolish#129 · Filter by author zhengyanstu opened on Mar 21, 2024

• polish_genome failed

  Nextomics/NextPolish#128 · Filter by author liuyca1 opened on Mar 15, 2024
  1

• [main_samview] fail to read the header from "-"

  Nextomics/NextPolish#126 · Filter by author kishor2019 opened on Dec 26, 2023
  1

• run fails with long read only in conda env

  Nextomics/NextPolish#124 · Filter by author splaisan opened on Nov 8, 2023
  5

• make[2]: *** [Makefile:30: bwa] Error 1 错误

  Nextomics/NextPolish#121 · Filter by author smoothyly opened on Oct 22, 2023
  1

• db_split failed:

  Nextomics/NextPolish#119 · Filter by author YDD99 opened on Aug 16, 2023
  4

• Test run failed at map_genome: "[gzclose] buffer error"

  Nextomics/NextPolish#117 · Filter by author jmpolinski opened on Jul 26, 2023
  3

• Ignore the secondary alignment

  Nextomics/NextPolish#116 · Filter by author lilinzhou opened on Jul 21, 2023
  2

• Empty bin directory after installation?

  Nextomics/NextPolish#112 · Filter by author JolandadeB opened on May 8, 2023
  2

• repeat regions

  Nextomics/NextPolish#111 · Filter by author cfz1998 opened on Mar 22, 2023
  5

• nextpolish2.py never stop

  Nextomics/NextPolish#108 · Filter by author yangfangyuan0102 opened on Feb 27, 2023
  6

• Using Illumina Hi-C and Chicago data?

  Nextomics/NextPolish#104 · Filter by author 000generic opened on Feb 5, 2023
  4

• Polish with raw or corrected ONT reads?

  Nextomics/NextPolish#102 · Filter by author tbrown91 opened on Oct 22, 2022
  1

• how to deal with "N"

  Nextomics/NextPolish#101 · Filter by author LINGLIU18 opened on Oct 21, 2022
  1

• Why there is no stats about changes when polished with nextpolish1.py or nextpolish2.py

  Nextomics/NextPolish#99 · Filter by author MongXR opened on Aug 4, 2022
  1

• Polish only INDELs or only SNPs, and polishing thresholds

  Nextomics/NextPolish#95 · Filter by author mmontonerin opened on Jun 13, 2022
  1

• slurm_submit_batch_job error

  Nextomics/NextPolish#92 · Filter by author scylaz opened on Apr 24, 2022
  1