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bacpop
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PopPUNK
PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
https://www.bacpop.org/poppunk
Apache License 2.0
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Update documentation to reflect new API (v2.3.0)
#122
johnlees
closed
3 years ago
0
Add lengths to network edges for visualisation
#121
johnlees
closed
3 years ago
3
Visualisation with assign query + lineage fit
#120
johnlees
closed
3 years ago
2
Ensure assign_query supports single query sequence
#119
johnlees
closed
3 years ago
0
Lineage sketchlib
#118
Danderson123
closed
3 years ago
0
Distances failed quality control (change QC options to run anyway)
#117
Rathanin-github
closed
3 years ago
2
Can I apply PopPUNK on metagenome assembled genomes
#116
SilasK
closed
3 years ago
1
Quick fix for query assign code
#115
johnlees
closed
3 years ago
0
popunk_sketch :: not found
#114
EricDeveaud
closed
3 years ago
2
No module named 'pp_sketchlib'
#113
EricDeveaud
closed
3 years ago
4
Move visualisation and assign query into their own programs
#112
johnlees
closed
3 years ago
4
Help/version is slow
#111
johnlees
closed
3 years ago
0
Uses new algorithm for clique pruning, which has better scaling
#110
johnlees
closed
3 years ago
0
genomes are duplicated
#109
SilasK
closed
3 years ago
6
Use pp-sketchlib for lineage assignment code
#108
johnlees
closed
3 years ago
1
Make assign query its own program
#107
johnlees
closed
3 years ago
0
poppunk --threshold raises error
#106
SilasK
closed
3 years ago
17
Distances failed quality control (change QC options to run anyway)
#105
furqan915
closed
3 years ago
8
Update to sketchlib v1.5.1
#104
johnlees
closed
3 years ago
0
Meta: Refactor code base
#103
johnlees
opened
3 years ago
2
Update to sketchlib v1.5.0
#102
johnlees
closed
3 years ago
0
Sample QC
#101
nickjcroucher
closed
4 years ago
1
Use QC information now stored in HDF5 files
#100
johnlees
closed
4 years ago
10
Error creating files for visualization
#99
d-golzato
closed
4 years ago
2
Accessory distance of zero for outlier samples
#98
lvclark
closed
4 years ago
3
Remove networkx from poppunk_references
#97
johnlees
closed
3 years ago
0
Floating point exception
#96
fasnicar
closed
4 years ago
4
Possible issue with taxa labelling in --lineage-clustering
#95
matbeale
closed
3 years ago
17
Improved default model refinement range
#94
johnlees
closed
4 years ago
0
Model refinement does not explore full relevant range
#93
nickjcroucher
closed
4 years ago
1
Combine sketchlib update with graph-tool implementation
#92
nickjcroucher
closed
4 years ago
0
Merge sketchlib140 into graph-tools
#91
nickjcroucher
closed
4 years ago
1
Update to pp-sketchlib v1.4.0
#90
johnlees
closed
4 years ago
2
Sample required densification?
#89
cizydorczyk
closed
4 years ago
3
can we run poppunk on a population containing different species within the same genus
#88
mabouelk
closed
4 years ago
1
GPU accelerated graphs
#87
johnlees
closed
3 years ago
5
Add interactivity to distance plot
#86
johnlees
opened
4 years ago
0
fitting model needs remove command
#85
pavlo888
closed
4 years ago
3
Add patristic distance calculation to extract distances script
#84
nickjcroucher
closed
3 years ago
0
Graph tool
#83
nickjcroucher
closed
4 years ago
3
Switch networkx for graph-tool
#82
johnlees
closed
4 years ago
5
Forthcoming issues with python 3.8.2
#81
nickjcroucher
closed
4 years ago
5
Parallelise distance matrix reshaping
#80
nickjcroucher
closed
4 years ago
5
Make lineage assignment into a model object
#79
johnlees
closed
3 years ago
1
Parallelise assignment functions
#78
johnlees
closed
4 years ago
5
Separate '--generate-viz' mode into an exported script.
#77
nickjcroucher
closed
3 years ago
0
Used sharedmemory in python v3.8
#76
johnlees
closed
4 years ago
0
Python version 3.8 and above - changes to multiprocessing
#75
nickjcroucher
closed
4 years ago
11
Update documentation
#74
johnlees
closed
3 years ago
1
Switch to docopt
#73
johnlees
closed
3 years ago
1
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