Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextomics/nextpolish issues and pull requests

#142 - nextPolish claims to be nextDenovo

Issue - State: closed - Opened by EricDeveaud about 1 month ago - 1 comment

#140 - Is there any option for unpolished Ns stay as Ns?

Issue - State: closed - Opened by hyunjokoo 4 months ago - 1 comment

#139 - polish for scaffod.fa(contain Ns)

Issue - State: open - Opened by DayTimeMouse 4 months ago

#138 - NextPolish for metagenome?

Issue - State: open - Opened by 123chenshixin 5 months ago - 1 comment

#137 - NextPolish fails with Short and Long Reads

Issue - State: closed - Opened by steinbrl 5 months ago - 1 comment

#136 - After the gap filling for scaffolds, using NextPolish.

Issue - State: closed - Opened by DayTimeMouse 5 months ago - 2 comments

#134 - The telemore sequences were removed after Nextpolish

Issue - State: open - Opened by YouxinZhao 6 months ago - 1 comment

#130 - The process of polishing causes a significant decrease in genome size.

Issue - State: open - Opened by xujialupaoli 10 months ago - 11 comments

#129 - problem with NextPolish-CentOS6.9.tgz

Issue - State: open - Opened by zhengyanstu 11 months ago

#128 - polish_genome failed

Issue - State: open - Opened by liuyca1 11 months ago - 1 comment

#127 - zlib.h not found error

Issue - State: closed - Opened by BRNiu 11 months ago - 1 comment

#126 - [main_samview] fail to read the header from "-"

Issue - State: open - Opened by kishor2019 about 1 year ago - 1 comment

#125 - SLURM out of memory and time...

Issue - State: closed - Opened by VendelboNM about 1 year ago - 1 comment

#124 - run fails with long read only in conda env

Issue - State: open - Opened by splaisan over 1 year ago - 5 comments

#123 - modifiy the associative array

Pull Request - State: open - Opened by jyw-atgithub over 1 year ago

#122 - slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT

Issue - State: closed - Opened by VendelboNM over 1 year ago - 1 comment

#121 - make[2]: *** [Makefile:30: bwa] Error 1 错误

Issue - State: open - Opened by smoothyly over 1 year ago - 1 comment

#120 - How does NextPolish polish an assembly with long reads?

Issue - State: closed - Opened by shelkmike over 1 year ago - 1 comment

#119 - db_split failed:

Issue - State: open - Opened by YDD99 over 1 year ago - 4 comments

#118 - Installation failure with multiple definition of 'rle_auxtab'

Issue - State: closed - Opened by tatsu1207 over 1 year ago - 3 comments

#117 - Test run failed at map_genome: "[gzclose] buffer error"

Issue - State: open - Opened by jmpolinski over 1 year ago - 3 comments

#116 - Ignore the secondary alignment

Issue - State: open - Opened by lilinzhou over 1 year ago - 2 comments

#115 - run nextplolish2.py sleep

Issue - State: closed - Opened by wang-zewen over 1 year ago - 8 comments

#114 - [question] combine with medaka or not?

Issue - State: closed - Opened by JWDebler over 1 year ago - 3 comments

#113 - User defined alignment pipeline for short- and long-reads

Issue - State: closed - Opened by RenscoHogers over 1 year ago - 2 comments

#112 - Empty bin directory after installation?

Issue - State: open - Opened by JolandadeB almost 2 years ago - 2 comments

#111 - repeat regions

Issue - State: open - Opened by cfz1998 almost 2 years ago - 5 comments

#110 - error of generate_lqseqs_from_cluster

Issue - State: closed - Opened by fangdm almost 2 years ago - 3 comments

#109 - Adding Hisat2 instead of BWA

Issue - State: closed - Opened by arslan9732 almost 2 years ago - 1 comment

#108 - nextpolish2.py never stop

Issue - State: open - Opened by yangfangyuan0102 almost 2 years ago - 6 comments

#107 - MissAssembly Correction using NextPolish (Need Suggestions)

Issue - State: closed - Opened by DrNavi almost 2 years ago - 1 comment

#105 - How to use Nextpolish on NextDenovo draft assembly

Issue - State: closed - Opened by DrNavi almost 2 years ago - 2 comments

#104 - Using Illumina Hi-C and Chicago data?

Issue - State: open - Opened by 000generic about 2 years ago - 4 comments

#103 - NextPolish slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT

Issue - State: closed - Opened by martinmau1 about 2 years ago - 6 comments

#102 - Polish with raw or corrected ONT reads?

Issue - State: open - Opened by tbrown91 over 2 years ago - 1 comment

#101 - how to deal with "N"

Issue - State: open - Opened by LINGLIU18 over 2 years ago - 1 comment

#100 - Reduction in genome size after polishing

Issue - State: closed - Opened by Shenu-Hudson over 2 years ago - 3 comments

#98 - gap filling effects?

Issue - State: closed - Opened by EugeneKim76 over 2 years ago - 2 comments

#97 - ImportError

Issue - State: closed - Opened by mergi-2674 over 2 years ago - 4 comments

#96 - NextPolish license and distribution of source code

Issue - State: closed - Opened by seb45tian over 2 years ago - 1 comment

#95 - Polish only INDELs or only SNPs, and polishing thresholds

Issue - State: open - Opened by mmontonerin over 2 years ago - 1 comment

#94 - How NextPolish v1.4 treat gap in genome ?

Issue - State: closed - Opened by Johnsonzcode almost 3 years ago - 1 comment

#93 - db_split errors

Issue - State: closed - Opened by k-williamson almost 3 years ago - 1 comment

#92 - slurm_submit_batch_job error

Issue - State: open - Opened by scylaz almost 3 years ago - 1 comment

#91 - No seq_split in new download

Issue - State: closed - Opened by Amarea1 almost 3 years ago - 5 comments

#90 - How long and how much memory should NextPolish require?

Issue - State: open - Opened by kcl58759 almost 3 years ago - 4 comments

#89 - db split1 issue

Issue - State: open - Opened by kcl58759 almost 3 years ago - 6 comments

#88 - Unable to run nextpolish program

Issue - State: open - Opened by amit4mchiba almost 3 years ago - 3 comments

#87 - Errors with nextPolish.sh.e

Issue - State: open - Opened by Gerlex89 about 3 years ago - 8 comments

#86 - Can I use the RNAseq data for genome polishing?

Issue - State: closed - Opened by CGsTree about 3 years ago - 2 comments

#85 - Some question about pacbio hifi data polish

Issue - State: closed - Opened by xiaobaiymq about 3 years ago - 6 comments

#84 - unable to create files for use for nextpolish.py from a offline method

Issue - State: closed - Opened by amit4mchiba about 3 years ago - 4 comments

#83 - NextPolish 1.4.0 does not complile with GCC 10 (under Debian 11)

Issue - State: closed - Opened by pvstodghill about 3 years ago - 3 comments

#82 - Missing .stats file ... ?

Issue - State: closed - Opened by josieparis over 3 years ago - 2 comments

#81 - Using Illumina reads containing "N" bases

Issue - State: closed - Opened by cgjosephlee over 3 years ago - 1 comment

#80 - Memory issue at index_genome

Issue - State: closed - Opened by rotoke over 3 years ago - 2 comments

#79 - Nextpolish on slurm

Issue - State: closed - Opened by aureliendejode over 3 years ago - 1 comment

#78 - nextPolish: "shutil.Error: Cannot move a directory onto itself"

Issue - State: closed - Opened by shankar2318 over 3 years ago - 1 comment

#77 - liblzma.so.0 not found

Issue - State: closed - Opened by gorliver over 3 years ago - 2 comments

#76 - Error when running test data

Issue - State: open - Opened by Amarea1 over 3 years ago - 1 comment

#75 - stuck at 03.kmer_count, seq_split outputs FASTA file instead of FASTQ

Issue - State: closed - Opened by ctxchris over 3 years ago - 5 comments

#74 - Samtools not finding libraries

Issue - State: closed - Opened by Neato-Nick over 3 years ago - 2 comments

#73 - Short reads pre-processing before polishing

Issue - State: open - Opened by aureliendejode over 3 years ago - 3 comments

#72 - make: *** [Makefile:18：all] 错误 2

Issue - State: closed - Opened by WJT0925 over 3 years ago - 1 comment

#71 - Illumina, HiFi, and Nanopore -- best strategy?

Issue - State: closed - Opened by StefanoLonardi almost 4 years ago - 3 comments

#70 - Error_report

Issue - State: open - Opened by kishor2019 almost 4 years ago - 2 comments

#69 - liblzma error

Issue - State: closed - Opened by kishor2019 almost 4 years ago - 2 comments

#68 - Problem with NextPolish for centos6.9

Issue - State: closed - Opened by misago162 about 4 years ago - 6 comments

#67 - nextPolish on Docker

Issue - State: open - Opened by marco91sol about 4 years ago - 1 comment

#66 - python2: ctg_cns.c:2787: find_sup_alns: Assertion `i != sup_aln->i' failed.

Issue - State: closed - Opened by lurebgi about 4 years ago - 4 comments

#65 - Could you provide an example how to use cluster_options?

Issue - State: open - Opened by MinjieHu about 4 years ago - 1 comment

#64 - BUSCO and LAI decrease after polish

Issue - State: open - Opened by Weihankk about 4 years ago - 1 comment

#63 - lower case introduced after nanopolish

Issue - State: closed - Opened by longzhangnation about 4 years ago - 2 comments

#62 - The meaning of "Max_depth"

Issue - State: closed - Opened by lilinzhou about 4 years ago - 1 comment

#61 - How many bases are corrected in each iteration?

Issue - State: closed - Opened by slbai01 about 4 years ago - 2 comments

#60 - How to rerun a unfinished job ?

Issue - State: closed - Opened by biozhangzhou about 4 years ago - 3 comments

#59 - Ploidy option in config file?

Issue - State: closed - Opened by cizydorczyk about 4 years ago - 2 comments

#57 - Running NextPolish on transcriptome?

Issue - State: open - Opened by xuesoso over 4 years ago - 1 comment

#56 - Using Mate-paired reads

Issue - State: closed - Opened by rmarquezp over 4 years ago - 2 comments

#55 - Exceplionally long run time for fungal genomes, is this normal?

Issue - State: closed - Opened by Rob-murphys over 4 years ago - 23 comments

#54 - How to polish with long reads and short reads in Single-End mode

Issue - State: open - Opened by gitcruz over 4 years ago - 5 comments

#53 - Single-End mode for polishing with illumina short reads

Issue - State: closed - Opened by gitcruz over 4 years ago - 1 comment

#52 - NextPolish Installation

Issue - State: open - Opened by marco91sol over 4 years ago - 1 comment

#51 - error with test data

Issue - State: closed - Opened by dtusso2020 over 4 years ago - 2 comments

#50 - using Nextpolish and after polished ,produce more contigs

Issue - State: open - Opened by guang-xi over 4 years ago - 4 comments

#49 - Nextpolish unfinished

Issue - State: open - Opened by Lcornet over 4 years ago - 3 comments

#48 - About the question for polishing long reads

Issue - State: open - Opened by MissLiXin over 4 years ago - 1 comment

#47 - type error '<' not supported between instances of 'str' and 'int'

Issue - State: closed - Opened by binlu1981 over 4 years ago - 1 comment
Labels: bug

#46 - short reads polishing stopped for the second round

Issue - State: open - Opened by longzhangnation over 4 years ago - 2 comments

#45 - What is a proper "-min_read_len" options?

Issue - State: closed - Opened by AntetokounmJie over 4 years ago - 2 comments

#44 - work with compressed fq file

Issue - State: closed - Opened by binlu1981 over 4 years ago - 1 comment

#43 - polishing strategy and rounds

Issue - State: open - Opened by binlu1981 over 4 years ago - 3 comments