malonge/RagTag

Issues

• The possibility of starting from HiFi ccs reads

  #192 opened 2 months ago by OceanLyu
  0

• integration with juicer

  #191 opened 2 months ago by Overcraft90
  0

• Scaffold option -r error

  #190 opened 3 months ago by arif-tanmoy
  0

• question of Hi-C to resolve conflicts

  #189 opened 3 months ago by njliangdong
  0

• patch output genome is identical to input target genome

  #175 opened a year ago by wackerk
  1

• `updategff` produces wrong output if parts of the scaffolds are used in the AGP file

  #188 opened 3 months ago by taprs
  0

• ragtag.patch.fasta lacks unplaced contigs?

  #185 opened 3 months ago by adadiehl
  1

• RagTag error: "OSError: error when opening file"

  #187 opened 4 months ago by ylzou867
  0

• Adjust default gap size

  #186 opened 5 months ago by mrvollger
  1

• a bytes-like object is required, not 'dict'

  #141 opened 2 years ago by mabh5
  8

• RagTag patch bug

  #155 opened 2 years ago by r-poloni
  4

• Missing ragtag.correct.reads.s.bam file

  #184 opened 5 months ago by faye-romero
  1

• Scaffold and correct

  #183 opened 6 months ago by aabaricalla
  1

• ragtag_scaffold.py: error: unrecognized arguments

  #182 opened 6 months ago by athenasyarifa
  0

• output file not found

  #181 opened 6 months ago by Anysdn
  0

• The scaffold command was submitted and the assembled result was not available

  #180 opened 6 months ago by LZY19940813
  1

• Ragtag.py merge RuntimeError: only complete components can be added to the graph error

  #156 opened 2 years ago by benyoung93
  6

• A question about "correct" step in RagTag, I need help!

  #158 opened 8 months ago by link-xhx
  3

• Using RagTag to close the gaps in a chromosome or reference genome using long-read data

  #179 opened 9 months ago by gforg34
  0

• Ragtag Merge IndexError for -f AGP file

  #177 opened a year ago by nickgladman
  0

• ERROR: encountered an invalid zero or negative numeric AGP field.

  #176 opened a year ago by wshuai294
  1

• correct use by the species.

  #163 opened 2 years ago by danielpinilla1
  1

• Can't use multiple threads via -t

  #171 opened a year ago by ChungLamYu
  3

• Error when running RagTag patch command

  #174 opened a year ago by nvuhunganh
  1

• pysam error

  #173 opened a year ago by mabh5
  0

• Scaffolding inserts gaps that aren't covered by HiFi or ONT reads and aren't in reference

  #170 opened a year ago by nickgladman
  7

• Scaffold longer than reference genome due to NNNNs

  #172 opened a year ago by vappiah
  3

• Scaffold inserting strings of 100 N's?

  #157 opened a year ago by cizydorczyk
  3

• the result of ragtag.merge.fasta shows no improvement.

  #169 opened a year ago by zhangkaihui1
  0

• `ragtag scaffold` without concatenation

  #168 opened a year ago by taprs
  0

• From delta file to agp and to fasta file of scaffolded assembly?

  #167 opened a year ago by hrpelg
  0

• updategff issues

  #166 opened a year ago by El-Castor
  0

• Stop without error message on "Reading whole genome alignments"

  #165 opened 2 years ago by Wzuoqi
  0

• RagTAg correct: "no attribute 'get_reference_length'"

  #162 opened 2 years ago by pna059
  1

• Unable to fill gap with ragtag scaffold and patch

  #164 opened 2 years ago by yipukangda
  0

• Question about installation

  #159 opened 2 years ago by zhousun21
  1

• Running RagTag on bacterial short-read assemblies

  #161 opened 2 years ago by ne1al
  0

• Large >270Mb contigs vs >14Gb reference

  #160 opened 2 years ago by Ural-Yunusbaev
  0

• Patch error: "Tuple Index out of Range"

  #152 opened 2 years ago by schmigle
  1

• Scaffolding error: 'RuntimeError: There are no useful alignments. Check output alignment files.`

  #145 opened 2 years ago by bahiyahazli
  3

• RagTag Reference

  #147 opened 2 years ago by WeixuanPlant
  1

• repeat masking

  #150 opened 2 years ago by evo-eco-gen
  1

• How to pass minimap2 parameters?

  #151 opened 2 years ago by evo-eco-gen
  1

• Cases where missassembly correction and patching aren't needed

  #153 opened 2 years ago by sjfleck
  1

• Scaffold doesn't run

  #154 opened 2 years ago by aebaci
  1

• RagTag name coming up

  #149 opened 2 years ago by rmormando
  0

• Some contigs are not scaffolded

  #148 opened 2 years ago by rknx
  0

• Error message when running ragtag_scaffold.py

  #146 opened 2 years ago by Surbhigrewal
  0

• about paf2delta

  #144 opened 2 years ago by 1085268616
  1

• Can RagTag use for improve assembled contigs from macrogenomes or macrotrasncriptome

  #143 opened 2 years ago by NailouZhang
  0