CarmenSheppard / PneumoKITy

PneumoKITy - Fast sensitive Pneumococcal Capsular Serotype screening from WGS data

CarmenSheppard/PneumoKITy Issues

singularity image
Updated 9 months ago1
raise KeyError(f"{not_found} not in index")
Closed 9 months ago2
df.append() depreciated
Updated 2 years ago1
Add feature to create % for mixture multiplicities
Closed 3 years ago1
18F reference sequence failing with <70% hit RED rag status
Closed 3 years ago1
onscreen info for serotype within groups
Closed 3 years ago1
"mixed serotypes" for 19F and 32F/A when not mixed
Closed 3 years ago1
Remove text from "predicted phenotype" field for group level detemination
Closed 3 years ago1
Check 25FA determination from ENA panel
Closed 3 years ago1
Median multiplicity as quality metric
Closed 3 years ago1
Update outputs to suit "pneumoKity"
Closed 4 years ago1
Filename checking for read 1 and read 2
Closed 4 years ago1
Add stage 2 for serogroup 25F/25A
Closed 4 years ago2
Stop low hits in stage 2 being flagged amber when gene not present"
Closed 4 years ago1
List index out of range interpreting serotype 39 result
Closed 4 years ago2
Collation not correctly collating all data
Closed 4 years ago2
Error writing empty dataframe
Closed 4 years ago2
add sample ID to stdout
Closed 4 years ago1
False Ctvdberror
Closed 4 years ago4
Check Mixed serotype determination - for hit and group in mix.
Closed 4 years ago1