Issues

• GPSv11 model database removing large number of AllTheBacteria pneumo samples during assignment QC

  bacpop/PopPUNK#379 · Filter by author samhorsfield96 opened on Aug 17, 2026
  1

• isolateNameToLabel fails when isolate names are numeric

  bacpop/PopPUNK#378 · Filter by author weichisyu opened on Aug 14, 2026

• [database] Pseudomonas aeruginosa db update with added genomes.

  enhancement
  bacpop/PopPUNK#377 · Filter by author jenzyy97 opened on Aug 6, 2026
  2

  

• Build kite broken

  bacpop/PopPUNK#364 · Filter by author johnlees opened on Nov 28, 2025
  2

• Runtime Error Performing Data Quality Control

  bacpop/PopPUNK#363 · Filter by author hillerlab217 opened on Nov 24, 2025
  1

• poppunk_assign ERROR samples are missing from the final network

  bacpop/PopPUNK#360 · Filter by author drhchen opened on Oct 11, 2025
  7

• poppunk_assign error

  bacpop/PopPUNK#359 · Filter by author zjx22018105-coder opened on Aug 27, 2025
  4

• Using pre-created kmer distances

  bacpop/PopPUNK#355 · Filter by author balags1 opened on Jul 3, 2025
  3

• missing .dists.npy

  bacpop/PopPUNK#353 · Filter by author vesa00 opened on Jun 10, 2025
  6

• segmentation fault with lineage model when multi-threading

  Bug

  bacpop/PopPUNK#352 · Filter by author dr-joe-wirth opened on Jun 5, 2025
  1

• Issues with the use of poppunk_visualise

  bacpop/PopPUNK#348 · Filter by author vesa00 opened on Mar 4, 2025
  1

• _Pseudomonas aeruginosa_ database error

  bacpop/PopPUNK#347 · Filter by author erinyoung opened on Jan 29, 2025
  3

• Support all network.py functions in CPU and GPU modes

  bacpop/PopPUNK#341 · Filter by author johnlees opened on Jan 6, 2025

• Question about de novo multi-species Nocardiopsis database

  enhancement
  bacpop/PopPUNK#339 · Filter by author ERBringHorvath opened on Dec 12, 2024
  2

  

• Add --qc-keep to poppunk_assign

  enhancement
  bacpop/PopPUNK#335 · Filter by author DOH-JDJ0303 opened on Oct 23, 2024
  1

• .dist.npy needed by poppunk --qc-db

  bacpop/PopPUNK#334 · Filter by author DOH-JDJ0303 opened on Oct 23, 2024
  1

• Taxon not beeing assigned correctly

  bacpop/PopPUNK#333 · Filter by author nermze opened on Oct 17, 2024
  6

• Improve network functions

  bacpop/PopPUNK#331 · Filter by author nickjcroucher opened on Oct 9, 2024
  

• Remove longtosquare from visualise

  bacpop/PopPUNK#329 · Filter by author johnlees opened on Sep 27, 2024

• poppunk iterate: raise TypeError("multiplier must be an int or float")

  bacpop/PopPUNK#323 · Filter by author luciagrami opened on Aug 22, 2024
  1

• Input reference list is misformatted

  bacpop/PopPUNK#310 · Filter by author SeqBioUCC opened on Apr 30, 2024
  10

• Cytoscape includes strains from the entire database even with the --include-files option

  bacpop/PopPUNK#309 · Filter by author sydelstan opened on Apr 25, 2024
  5

• Issue with a large Pseudomonas dataset

  bacpop/PopPUNK#299 · Filter by author RyanCFink opened on Jan 16, 2024
  4

• Zero Accessory Distances and Varied Core Distances in PopPUNK Fit Graph Analysis

  question
  bacpop/PopPUNK#289 · Filter by author RyanCFink opened on Nov 24, 2023
  8

• Enhancement: Assigning multiple GPSC types to mixed (meta-genome) samples

  enhancementwontfix
  bacpop/PopPUNK#287 · Filter by author sreerampeela opened on Nov 13, 2023
  2