gtonkinhill/panaroo

Issues

• Visualizing Panaroo Results

  #313 opened a month ago by AzizHN
  2

• Sporadic KeyError exceptions raised during collapse_families

  #307 opened 3 months ago by revinici
  4

• Panaroo Processing Inquiry

  #311 opened 2 months ago by AzizHN
  1

• Some gene alignments in aligned_gene_sequences/ have fragmented entries

  #312 opened 2 months ago by mudymudy
  1

• Panaroo reporting genes of very different lengths together in the same gene family - Expected Behaviour?

  #299 opened 2 months ago by NickJD
  12

• Biopython deprecation error

  #301 opened 2 months ago by lucyjanekelly
  4

• Add functionality to batch gene alignments

  #306 opened 2 months ago by revinici
  4

• panaroo merge does not produce combined_protein_CDS.fasta

  #308 opened 2 months ago by revinici
  2

• Broken error handling in multithread_codonalign_build

  #310 opened 2 months ago by revinici
  1

• Low number of genes as output

  #309 opened 2 months ago by AzizHN
  1

• Potential bug in panaroo

  #303 opened 2 months ago by Hocnonsense
  1

• Update the gene name in results of panaroo by bakta

  #305 opened 2 months ago by mook-monk
  1

• Get Multifasta or alignment for each CDSs

  #302 opened 2 months ago by nbat64
  1

• How to find paralog gene sequence in pan_genome_reference.fa?

  #304 opened 2 months ago by mai-rui-gao
  2

• Cd-hit-est problem

  #285 opened 3 months ago by anagaga27
  5

• Default CD-HIT length different percent different than displayed in help message

  #300 opened 4 months ago by Danderson123
  2

• Panaroo run time

  #290 opened 4 months ago by anuradhasingh15
  4

• cut-off of 100% aa identity not working properly

  #286 opened 4 months ago by memoriasresiduais
  1

• Gene clusters annotation

  #294 opened 4 months ago by anaGaGa98
  1

• Invalid file extension

  #295 opened 4 months ago by MHassanSaeed
  1

• Not running with prokka generated gff files

  #296 opened 4 months ago by EdwinDNavarroMonserrat
  4

• "NameError: Duplicate entry!!!" with a specific GenBank genome

  #298 opened 4 months ago by qianxuans
  1

• provide separate gff and fasta files as input for panaroo

  #297 opened 5 months ago by sun-qibo
  2

• Gene sequences alignment

  #293 opened 6 months ago by thorcs1
  2

• What to do with "xx_refound_yy" items in gene matrix?

  #292 opened 6 months ago by Asylulan
  0

• Recovering gene coordinates

  #291 opened 6 months ago by theodorross
  2

• Request for Assistance in Identifying Core Genome from Result Files

  #289 opened 7 months ago by 2021JohnSheng
  2

• Increase in processing time

  #284 opened 7 months ago by anagaga27
  4

• Continue from concatenate_core_genome_alignments?

  #287 opened 7 months ago by qianxuans
  4

• Query Regarding Discrepancy in Output Information for Dataset of 3245 GFF3 Files

  #288 opened 7 months ago by 2021JohnSheng
  2

• Discrepency between final_graph.gml and gene_presence_absence.csv

  #276 opened 8 months ago by sydelstan
  4

• Bakta GFFs with --remove-invalid-genes still throw 'invalid gene!' error, doesn't get to alignment

  #279 opened 8 months ago by amyecampbell
  2

• Alternative start codon GTG translated as Val instead of Met

  #274 opened 8 months ago by cednotsed
  5

• Refound Genes Exhibit In-Frame Stops and Frameshifts: Seeking User-Friendly Controls and Improved Understanding for Downstream Analysis

  #263 opened 8 months ago by NickJD
  8

• UnboundLocalError: local variable 'prot_outname' referenced before assignment

  #278 opened 8 months ago by fengyuchengdu
  5

• Example of missing AMR gene allele

  #275 opened 8 months ago by Danderson123
  5

• Genes missing in the pangenome reference fasta

  #277 opened 8 months ago by LucoDevro
  2

• Overly-long gene names cause panaroo-extract-gene to fail

  #271 opened 8 months ago by cednotsed
  3

• Can't use panaroo of reference genomes annotated with prokka

  #268 opened 9 months ago by AnnaLew
  4

• List text file input method not working

  #265 opened 9 months ago by lillycummins
  6

• gene presence/absence file having ";" without merging paralogs

  #257 opened 9 months ago by mhjonathan
  3

• Interpretation of Gene Names and Downstream Analysis in Panaroo Pan-genome Studies

  #262 opened 9 months ago by luobosi
  1

• Some problem about panaroo's result

  #255 opened 9 months ago by Bin-Ma
  6

• clustered_proteins file in output?

  #266 opened 9 months ago by qianxuans
  1

• Wrong IDs in pangenome reference fasta

  #269 opened 9 months ago by LucoDevro
  3

• RuntimeError: Error reading prokka input!

  #261 opened 9 months ago by mabouelk
  4

• Error after while processing paralogs?

  #264 opened 10 months ago by bpeacock44
  7

• Failure of `panaroo-merge` with `-a core`

  #258 opened a year ago by HarryHung
  3

• error reading bakta gff3 files, conversion to prokka gff to make it working with panaroo 1.3.0

  #259 opened a year ago by FTouzain
  3

• A limit in number of input files?

  #256 opened a year ago by dianalaucw
  2