bacpop PopPUNK issues - Githubissues

bacpop / PopPUNK

PopPUNK 👨‍🎤 (POPulation Partitioning Using Nucleotide Kmers)

https://www.bacpop.org/poppunk

Apache License 2.0

86 stars 17 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

distance calculations hang forever

#316 rderelle closed 1 day ago
7
Update cluster assign to write qcreport on qc failiures

#315 absternator closed 1 day ago
0
Versions of input databases sketches are different and the network file choice for Cytoscape visualization

#314 RuwiniK opened 4 weeks ago
5
poppunk_visualise unable to find sequence in clustering

#313 fgonzalez3 closed 3 weeks ago
2
Update from master branch

#312 nickjcroucher closed 1 month ago
0
issues with assigning GPSCs

#311 johnlees opened 1 month ago
4
Input reference list is misformatted

#310 SeqBioUCC opened 2 months ago
10
Cytoscape includes strains from the entire database even with the --include-files option

#309 sydelstan opened 2 months ago
5
Unable to create the group "/sketches/": (Links) Object already exists

#308 danielarothschild closed 3 months ago
2
Output external clusterings with visualisations

#307 nickjcroucher closed 3 months ago
2
Update viz fix

#306 nickjcroucher closed 3 months ago
0
Avoid overwriting external clustering in visualise script

#305 nickjcroucher closed 3 months ago
1
Update plotting and network summary statistics

#304 nickjcroucher opened 4 months ago
0
Update graph summary processes

#303 nickjcroucher closed 4 months ago
0
Updates to DBSCAN fitting

#302 nickjcroucher closed 4 months ago
7
Improvements to DBSCAN fitting

#301 nickjcroucher closed 4 months ago
0
Listeria monocytogenes database is missing graph file.

#300 DOH-JDJ0303 closed 4 months ago
7
Issue with a large Pseudomonas dataset

#299 RyanCFink opened 5 months ago
4
Poppunk assign fix

#298 samhorsfield96 closed 6 months ago
0
Add permissions again

#297 johnlees closed 6 months ago
0
Remove permissions and add CNAME

#296 johnlees closed 6 months ago
0
Use gha to publish docs

#295 johnlees closed 6 months ago
0
Rename docs action

#294 johnlees closed 6 months ago
0
Add actions for docs build

#293 johnlees closed 6 months ago
0
Add the roadmap to the docs

#292 johnlees closed 7 months ago
0
Update readthedocs config file to v2

#291 johnlees closed 7 months ago
0
Update assign.py

#290 samhorsfield96 closed 7 months ago
0
Zero Accessory Distances and Varied Core Distances in PopPUNK Fit Graph Analysis

#289 RyanCFink opened 7 months ago
8
Update from master

#288 nickjcroucher closed 7 months ago
0
Enhancement: Assigning multiple GPSC types to mixed (meta-genome) samples

#287 sreerampeela opened 7 months ago
2
Remove deprecated system packages from readthedocs build

#286 johnlees closed 8 months ago
1
API change in mpl380 ellipses

#285 johnlees closed 8 months ago
0
Generating jaccard distances per kmer

#284 JLC2141 closed 9 months ago
3
PackagesNotFoundError

#283 RoyUnderwoodAbramski closed 9 months ago
2
Fix overwrite, correct error messages

#282 HarryHung closed 9 months ago
0
What to expect for a sample that may have a mixture of two or more strains

#281 ilyavs closed 10 months ago
2
extract genome assemblies from database

#280 reaset41 closed 10 months ago
1
Allow overwrite if forced

#279 johnlees closed 8 months ago
5
Sketchlib back end not available?

#278 hayleyjaywilson opened 11 months ago
8
ImportError: dlopen: cannot load any more object with static TLS

#277 davidtong28 opened 11 months ago
4
Update H. flu database to new sklearn version

#276 conmeehan opened 11 months ago
2
Add tutorial to documentation

#275 johnlees opened 11 months ago
0
Improve manual installation instruction

#274 HarryHung closed 11 months ago
0
IndexError: list index out of range (running current `master` branch) when running `poppunk_assign`

#273 HarryHung closed 7 months ago
25
Update CI to new mamba action

#272 johnlees closed 11 months ago
0
Update Git Repository link

#271 HarryHung closed 12 months ago
0
bacpop-133 Add pycairo dependency

#270 EmmaLRussell closed 5 months ago
1
databases: reference only vs all genomes

#269 sapuizait closed 7 months ago
1
Incorrect merge reporting from novel queries step

#268 johnlees closed 1 year ago
1
[database] A double-checked database of Neisseria meningitidis

#267 tanzhizhou closed 4 months ago
8