pangenome/pggb

Issues

• Follow up on issues with Singularity

  #404 opened 3 months ago by cjfields
  6

• Invalid argument on log file

  #412 opened a month ago by vikshiv123
  15

• Parameters optimization

  #360 opened a month ago by omar-almolla209
  1

• mismatched line lengths at line 3 within sequence

  #398 opened a month ago by Ahmad-40
  1

• PGGB singularity vg deconstruct not recognizing sample prefix

  #399 opened 6 months ago by SimonaSecomandi
  1

• Unable to generate giraffe indexes for PGGB graph

  #400 opened a month ago by KopalliV
  1

• wfmash to speed up

  #403 opened a month ago by OZTaekOppa
  1

• vcfwave not found

  #312 opened a month ago by aijigekoukou-shen
  3

• The question about `vg` version of pggb

  #415 opened 2 months ago by zwh82
  5

• pggb: option requires an argument -- 'i'

  #379 opened 2 months ago by RobStr12
  1

• PGGB takes more than 96 hours of walltime on HPC

  #407 opened 3 months ago by kiratalreja3
  1

• How to handle plasmid sequences for bacterial assemblies

  #406 opened 3 months ago by UpalabdhaD
  0

• Recommended practices for downstream analyses

  #394 opened 7 months ago by agolicz
  0

• erro about paf2net.py

  #393 opened 7 months ago by unavailable-2374
  2

• Memory size required to build large genomes

  #385 opened 8 months ago by Lucio-Yang
  14

• run without errors and outputs

  #388 opened 8 months ago by Gon1976
  7

• For aligning chromosomes of different species over 100MYA or div is it better to use .masked files?

  #383 opened 8 months ago by Isoris
  0

• the effect of `n_mappings`

  #382 opened 8 months ago by subwaystation
  0

• seqwish fails when `--output-dir` contains commas

  #356 opened a year ago by kdm9
  1

• what dose "consensus path" generated with parameter -Q mean

  #378 opened 8 months ago by yipukangda
  2

• A null vcf file

  #377 opened 8 months ago by dudududu12138
  3

• Command terminated by signal 6

  #374 opened 8 months ago by yeeus
  4

• Setting the poa-length-target(s)

  #375 opened 9 months ago by jonahcullen
  0

• container creation failed

  #373 opened 9 months ago by yeeus
  0

• computational efficiency of pggb

  #370 opened 10 months ago by yihangs
  3

• Gradual increase of pan-genomes

  #364 opened a year ago by Tonitsk8264
  1

• [help] My reference genome of a diploid organism is a primary assembly

  #363 opened a year ago by Isoris
  3

• How to visulize PGGB graph in Sequence Tube Map?

  #353 opened a year ago by arslan9732
  0

• Command terminated by signal 8

  #345 opened a year ago by clemgoub
  2

• vg deconstruct error

  #344 opened a year ago by arslan9732
  5

• --n-haplotypes option not recognized

  #342 opened a year ago by arunisaac
  2

• [docker] wfmash: error while loading shared libraries: libwfa2cpp.so.0

  #339 opened a year ago by clemgoub
  1

• 'SN:Z' and 'SO:i' tags for segments/nodes

  #328 opened a year ago by songbowang125
  1

• the parameters to build pangenome for metagenomes

  #337 opened a year ago by zwh82
  2

• Construct PanGenome

  #331 opened a year ago by Tonitsk8264
  7

• How to handle when two contigs from the same assembly sligtly overlap

  #329 opened a year ago by Isoris
  7

• How to understand the vcf file output by PGGB？

  #334 opened a year ago by Lucio-Yang
  3

• Use of pggb to generate alignments for phylogenomics

  #319 opened a year ago by sivico26
  2

• Building a better pangenome

  #306 opened a year ago by GeorgeBGM
  25

• Path to paf2net.py not correct in latest Docker build

  #322 opened a year ago by brettChapman
  2

• Wrong setting of POA, but it still finish without error

  #320 opened a year ago by baozg
  4

• Even if the genome is small, shouldn't too many samples be added to build the graph

  #316 opened a year ago by Wwwwwwwyc
  8

• Command terminated by signal 11

  #301 opened a year ago by Sh1ne111
  9

• Problem with the ODGI 1D visualization by path orientation

  #308 opened a year ago by KopalliV
  6

• Producing subgraphs of large pangenomes

  #309 opened a year ago by ASLeonard
  2

• Problems with skipping the wfmash step

  #314 opened a year ago by Lucio-Yang
  8

• Construct pangenome

  #313 opened a year ago by Daishoulu
  3

• Converting to a single connected component

  #310 opened a year ago by JoshuaDanielRubin
  2

• Joining the Chromosome Alignments？

  #307 opened a year ago by zskey-zn
  2

• The graph does not look quite the same as the collinear results

  #302 opened a year ago by Wwwwwwwyc
  7