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WGS-TB
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PathOGiST
This repository contains the pipeline for the multi-criterion genomic analysis of bacterial pathogens
GNU General Public License v3.0
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Unclear which snippy output file to provide to `PATHOGIST distance`
#35
sean-la
opened
5 years ago
0
Current conda package has too many dependencies
#34
sean-la
opened
5 years ago
0
MentaLiST installation in conda package has `LoadError`
#33
sean-la
opened
5 years ago
7
Mentalist path
#32
jwcodee
closed
5 years ago
0
PathOGiST build is failing
#31
sean-la
closed
5 years ago
8
Problem with PathOGiST conda build 0.3.2
#30
sean-la
closed
5 years ago
1
Update integration_test.sh
#29
jwcodee
closed
5 years ago
0
Spotying unzipped
#28
jwcodee
closed
5 years ago
0
Spotying unzipped
#27
jwcodee
closed
5 years ago
0
Travis genotype
#26
jwcodee
closed
5 years ago
0
Spotyping install
#25
jwcodee
closed
5 years ago
0
Mentalist install
#24
jwcodee
closed
5 years ago
0
Parallelize correlation clustering
#23
sean-la
opened
5 years ago
1
activated fastq check. only checking lines
#22
jwcodee
closed
5 years ago
0
Genotype of john
#21
jwcodee
closed
5 years ago
0
Check Fastq inputs
#20
jwcodee
closed
5 years ago
1
Use agg for visualization
#19
matnguyen
closed
5 years ago
0
Assert Config Inputs
#18
jwcodee
closed
5 years ago
1
Consensus Clustering Generating Inconsistent Results
#17
jwcodee
closed
5 years ago
1
Combined New Master to current dev
#16
jwcodee
closed
5 years ago
0
Enable C4 as default
#15
matnguyen
closed
5 years ago
0
Correlation Merge
#14
jwcodee
closed
5 years ago
0
Kwip (load_into-counting) option and genotyping options
#13
jwcodee
closed
5 years ago
0
Remove cplex as dependency
#12
matnguyen
closed
5 years ago
0
In `consensus` subcommand, modify all distance matrices to be on the same set of samples.
#11
sean-la
closed
5 years ago
0
Make `visualize` subcommand compatible with jupyter notebook
#10
sean-la
opened
5 years ago
0
Refactor `consensus` subcommand to take a YAML configuration file as input, similar to subcommand `all`.
#9
sean-la
opened
5 years ago
0
Dev johnathan
#8
jwcodee
closed
5 years ago
1
Bed File filter for SNP Distance Generation in
#7
jwcodee
closed
5 years ago
1
Spoligotype Distance Matrix Generation
#6
jwcodee
closed
5 years ago
2
Consensus clustering output should have the same column name as Correlation clustering
#5
pedrofeijao
opened
5 years ago
0
Add Pathogist to Bioconda
#4
matnguyen
closed
5 years ago
3
Reading calls file does not work with Galaxy
#3
matnguyen
closed
5 years ago
2
Calls Path file format
#2
matnguyen
closed
5 years ago
2
Galaxy interprets logger output to stderr as an actual error
#1
matnguyen
opened
5 years ago
2