gtonkinhill/panaroo

Issues

• Distinction between gene cluster names separated by "~~~" and "group_##".

  #254 opened a year ago
  2

• cd-hit error in first run of Panaroo

  #253 opened a year ago
  1

• Parallize pre-processing

  #252 opened a year ago
  1

• ERROR when writing output: double free or corruption (!prev): 0x000055f18142deb0

  #251 opened a year ago
  2

• Clustering id confirmation

  #250 opened a year ago
  2

• presence absence grid question

  #249 opened a year ago
  3

• Discrepancy in Gene Counts between summary_statistics.txt, pan_genome_reference.fa, and gene_presence_absence.csv

  #248 opened a year ago
  4

• Re turned non-zero exit status 1.

  #247 opened a year ago
  10

• What does "~~~" mean in the gene_presence_absence.csv file?

  #246 opened a year ago
  1

• Conda installation: pkg_resources module not found

  #245 opened a year ago
  1

• Unable to produce aln file

  #244 opened a year ago
  5

• Add a descriptive error message when you have 0 core genes

  #243 opened a year ago
  1

• cd-hit error

  #241 opened 2 years ago
  3

• Warning or error?

  #240 opened 2 years ago
  2

• Error while generating gffs from panaroo output

  #239 opened 2 years ago
  4

• What do the tildes (~) mean in the gene name column from the gene_presence_absence.csv output file?

  #238 opened 2 years ago
  1

• Issue installing panaroo on Mac M1 with Ventura

  #237 opened 2 years ago
  10

• Not recognising gff files

  #236 opened 2 years ago
  0

• Problems with multithreading

  #235 opened 2 years ago
  3

• Wrong information in the gene_presence_absence.Rtab file

  #234 opened 2 years ago
  2

• Problem processing non-NCBI generated GBK files

  #233 opened a year ago
  5

• Incomplete Panaroo output

  #232 opened 2 years ago
  1

• unconnected nodes

  #231 opened 2 years ago
  2

• Errno2 No such file or directory: '##gff-version'

  #230 opened 2 years ago
  2

• Genes present in prokka gff files but present as group_xxx in gene_presence_absence_file

  #228 opened 2 years ago
  2

• GFF3 from GenBank

  #227 opened 2 years ago
  1

• Bio.Alphabet module has been removed from Biopython error

  #226 opened 2 years ago
  3

• family threshold parameter and different proteins

  #225 opened 2 years ago
  2

• Conda build outdated (Bio.Alphabet issue)

  #224 opened 2 years ago
  3

• Uncollapsed gene families

  #223 opened 2 years ago
  1

• Question regarding alignment output and -a pan

  #220 opened 2 years ago
  5

• panaroo-extract-gene

  #219 opened 2 years ago
  1

• Trouble with Panaroo output

  #218 opened 2 years ago
  1

• Pangenome graph has single unconnected COGs

  #217 opened 2 years ago
  1

• How to plot a simple pangenome accumulation curve (numb genes vs numb genomes) using the output of panaroo?

  #216 opened 2 years ago
  3

• Error while collapsing gene families

  #215 opened 2 years ago
  4

• Error / processing paralogs -> collapse mistranslations

  #214 opened 2 years ago
  8

• duplicated clusters with same gene annotations

  #213 opened 2 years ago
  1

• Error with panaroo-generate-gffs

  #212 opened 2 years ago
  5

• Unmatched aligned gene location on gff and panaroo graph

  #211 opened 2 years ago
  4

• gene names separated by ~~~

  #210 opened 2 years ago
  2

• Meaning of multiple prokka IDs in a cell in presence/absence.csv?

  #209 opened 2 years ago
  1

• Question: What are the parameters in IMG output?

  #208 opened 2 years ago
  1

• Question about multithreading during paralog phase

  #207 opened 2 years ago
  3

• Problem reading data from RefSeq

  #206 opened 2 years ago
  5

• the form of core genes in gene_presence_absence.Rtab

  #205 opened 2 years ago
  1

• Using PRANK causes thousands of tmp fastas to be written in working directory

  #204 opened 2 years ago
  3

• core genome

  #203 opened 2 years ago
  5

• Panaroo version in bioconda is 1.1.2

  #202 opened 2 years ago
  1

• Error reading GFF produced by Bakta

  #201 opened 2 years ago
  5