malonge/RaGOO

Issues

• I have encountered the following errors when using this software. Can you help me solve them.

  #83 opened a year ago by zhangkaihui1
  0

• How to understad output ?

  #82 opened 3 years ago by YuChrming
  1

• RuntimeError: Failed

  #81 opened 4 years ago by luo123675
  2

• Unconventional Use of RagTag

  #80 opened 4 years ago by goeckeritz
  3

• Requiring specific mapping segment lengths

  #79 opened 4 years ago by selasphoruskershaw
  4

• how ragoo to set max_variant_size?

  #78 opened 4 years ago by qbdong
  1

• New sequence header

  #77 opened 4 years ago by vappiah
  11

• Unplaced sequences

  #76 opened 4 years ago by vappiah
  1

• PLASMIDS

  #75 opened 4 years ago by vappiah
  7

• make_agp.py not corresponding to ragoo.fasta

  #74 opened 4 years ago by jun3234
  4

• Difference between RaGOO and RagTag

  #73 opened 4 years ago by XMTian
  2

• "*.contig.fa.misasm.break.fa" may be a binary file.

  #69 opened 5 years ago by ShuaishuaiTai
  4

• Input as scaffolds

  #64 opened 4 years ago by tk2
  1

• unable to detect data files for Ragoo

  #62 opened 4 years ago by jainv45
  4

• ValueError: invalid literal for int() with base 10: '653057_RaGOO'

  #71 opened 4 years ago by neel404
  4

• How to use the short PE reads in the -R parameter

  #70 opened 4 years ago by ShuaishuaiTai
  1

• bed file for sequences aligned on the reference genome

  #68 opened 5 years ago by uggulhan
  1

• Some question about long sequence

  #72 opened 5 years ago by AntetokounmJie
  6

• Hard-coded output directory

  #34 opened 5 years ago by dariober
  3

• [morecore] insufficient memory

  #33 opened 5 years ago by mictadlo
  9

• Why BUSCO reports fewer genes after RaGOO?

  #66 opened 5 years ago by Ural-Yunusbaev
  5

• SPAdes + RaGOO

  #67 opened 5 years ago by francicco
  3

• RuntimeWarning: Mean of empty slice

  #65 opened 5 years ago by XuewenWangUGA
  5

• RaGOO - minimap2 runtime error

  #63 opened 5 years ago by RG-UCSB
  6

• Output directory name parameter

  #61 opened 5 years ago by ViriatoII
  2

• KeyError in get_contigs_border.py

  #60 opened 5 years ago by maherrl
  1

• ValueError in filter_gap_SVs.py (get_query_bed_coords)

  #59 opened 5 years ago by alexisnorris
  10

• SyntaxError: invalid syntax

  #57 opened 5 years ago by droeatumn
  3

• Estimation of real gap size

  #58 opened 5 years ago by soungalo
  1

• Output contig locations bed file

  #56 opened 5 years ago by soungalo
  6

• Liftover reference gff

  #55 opened 5 years ago by soungalo
  1

• Targeted assembly. Whole genome or target area as reference?

  #54 opened 5 years ago by ViriatoII
  1

• Why did it go to Chr0?

  #53 opened 5 years ago by soungalo
  3

• reassembling chr0

  #41 opened 5 years ago by mictadlo
  5

• Differentiation Pseudomolecules

  #52 opened 5 years ago by mwylerCH
  1

• Lift-over reference annotations to ordered contigs

  #51 opened 5 years ago by charlesfeigin
  2

• RaGOO Chr > reference Chr

  #50 opened 5 years ago by mazepago
  1

• Structural Variants Calling

  #49 opened 5 years ago by MehmetGoktay
  1

• Gap filling with RaGOO

  #48 opened 5 years ago by ViriatoII
  2

• FileNotFoundError: [Errno 2] No such file or directory:

  #46 opened 5 years ago by zhuangfjnu
  3

• option -i doesn't seam to work

  #47 opened 5 years ago by lalalagartija
  0

• Pseudomolecules creation step error

  #45 opened 5 years ago by Yedomon
  3

• Super-scaffolding two genome drafts

  #44 opened 5 years ago by enormandeau
  6

• RuntimeError when turing on the SV calling option

  #42 opened 5 years ago by JunpengShi
  4

• Maximum number of breaks per contig

  #43 opened 5 years ago by gbdias
  3

• Potential chimeric contig persists after RaGOO

  #35 opened 5 years ago by gbdias
  8

• RaGOO out visualization

  #40 opened 5 years ago by Ural-Yunusbaev
  8

• Preventing Ragoo output to be similar too reference

  #36 opened 5 years ago by mictadlo
  5

• Error in install

  #38 opened 5 years ago by shehongbing
  5

• Question: contig names in output

  #37 opened 5 years ago by reubwn
  1