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ktmeaton
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ncov-recombinant
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
MIT License
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sc2rf mode alternative hypothesis
#192
ktmeaton
closed
1 year ago
0
False positives caused by sc2rf XAJ mode
#191
ktmeaton
closed
1 year ago
2
Add documentation about edge cases (XN, XP, XAS, XAR, XAZ)
#190
ktmeaton
closed
1 year ago
1
CI: Migrate actions that use node12 to node16
#189
ktmeaton
opened
1 year ago
3
Remove breakpoint distribution axis
#188
ktmeaton
closed
1 year ago
1
AttributeError: 'Series' object has no attribute 'split
#187
ktmeaton
closed
1 year ago
0
proposed1252
#186
ktmeaton
closed
1 year ago
1
Use nextclade dataset Auspice tree for lineage hierarchy
#185
ktmeaton
closed
1 year ago
2
XBB.1.2
#184
ktmeaton
closed
1 year ago
0
Recombinant sublineages
#183
ktmeaton
closed
1 year ago
1
XBC.2
#182
ktmeaton
closed
1 year ago
0
XBC.1
#181
ktmeaton
closed
1 year ago
0
Recombinant sublineages (ex. XAY.1) are missing their derived mutations in the cov-spectrum query
#180
ktmeaton
closed
1 year ago
0
sc2rf recombinants.ansi.txt is truncated
#179
ktmeaton
closed
1 year ago
0
XAY.1
#178
ktmeaton
closed
1 year ago
0
XBE
#177
ktmeaton
closed
1 year ago
4
Upgrade Nextclade dataset
#176
ktmeaton
closed
1 year ago
1
XBB.1.1
#175
ktmeaton
closed
1 year ago
0
XBB.3
#174
ktmeaton
closed
1 year ago
1
XBB.2
#173
ktmeaton
closed
1 year ago
0
XBB.1
#172
ktmeaton
closed
1 year ago
0
XBD
#171
ktmeaton
closed
1 year ago
0
Use conda-forge channel instead of anaconda for environment
#170
ktmeaton
closed
1 year ago
1
AttributeError: 'str' object has no attribute 'name'
#169
ktmeaton
closed
1 year ago
1
Investigate allowing NULL collection dates (NA)
#168
ktmeaton
closed
1 year ago
3
Alias key out of date, change source
#167
ktmeaton
closed
1 year ago
0
proposed1138
#166
ktmeaton
closed
1 year ago
1
proposed1139
#165
ktmeaton
closed
1 year ago
0
False positives appearing in recombinants.ansi.txt
#164
ktmeaton
closed
1 year ago
0
Change LAPIS mutation query from pangoLineage to nextcladePangoLineage
#163
ktmeaton
closed
1 year ago
1
Upgrade sc2rf virus_properties 2022-09-27
#162
ktmeaton
closed
1 year ago
5
Experiment with override of sc2rf_recombinants and postprocess
#161
ktmeaton
closed
1 year ago
1
XBC
#160
ktmeaton
closed
1 year ago
0
Upgrade nextclade dataset to 2022-09-27
#159
ktmeaton
closed
1 year ago
0
Reduce sc2rf --max-intermission-length to 2
#158
ktmeaton
closed
1 year ago
0
Create parameters for min-lineage-size and max-private-muts in linelist
#157
ktmeaton
closed
1 year ago
0
Legend has too few columns
#156
ktmeaton
closed
1 year ago
1
GISAID Controls
#155
ktmeaton
closed
1 year ago
0
GISAID Data for GitHub Continuous Integration
#154
ktmeaton
closed
1 year ago
2
Path specification of metadata and sequences is not implemented
#153
ktmeaton
closed
1 year ago
0
OSError: Cannot save file into a non-existent directory
#152
ktmeaton
closed
1 year ago
0
Samples missing from linelists when they fail alignment
#151
ktmeaton
closed
1 year ago
1
sc2rf writes empty output csvfiles if no recombinants found
#150
ktmeaton
closed
1 year ago
0
XA
#149
ktmeaton
closed
1 year ago
0
XB
#148
ktmeaton
closed
1 year ago
0
XC
#147
ktmeaton
closed
1 year ago
0
XD
#146
ktmeaton
closed
1 year ago
0
XE
#145
ktmeaton
closed
1 year ago
0
XF
#144
ktmeaton
closed
1 year ago
0
XG
#143
ktmeaton
closed
1 year ago
0
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