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mbhall88
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head_to_head_pipeline
Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
GNU General Public License v3.0
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RIF and INH off-catalogue mutations
#85
mbhall88
closed
2 years ago
6
Update repository READMEs
#84
mbhall88
closed
2 years ago
0
Submit data to the ENA
#83
mbhall88
closed
1 year ago
5
Mutation concordance analysis
#82
mbhall88
closed
2 years ago
9
Try mykrobe with a lower proportion of expected depth
#81
mbhall88
closed
2 years ago
4
Rebasecall nanopore data with guppy v5.0.16
#80
mbhall88
closed
2 years ago
12
Nanopore homopolymer deletions in katG
#79
mbhall88
closed
2 years ago
2
Visualise available phenotype information
#78
mbhall88
closed
3 years ago
3
De novo SNP discovery in resistance genes
#77
mbhall88
closed
2 years ago
3
Concordance of resistance predictions with phenotype
#76
mbhall88
closed
3 years ago
15
Concordance of resistance predictions with Illumina
#75
mbhall88
closed
3 years ago
28
Run mykrobe on all samples
#74
mbhall88
closed
3 years ago
0
Get coverage info for all samples
#73
mbhall88
closed
3 years ago
2
Create sample resistance reference sheet
#72
mbhall88
closed
3 years ago
1
Compare trees generated by mixed technology, with that from illumina/compass
#71
iqbal-lab
closed
1 year ago
1
Mixed technology distances
#70
mbhall88
closed
3 years ago
15
Are all repeats samples clustered together
#69
mbhall88
closed
3 years ago
9
Investigate R28980 & R20574 sample swap
#68
mbhall88
closed
3 years ago
10
Code script to go from pandora VCF to DST result
#67
mbhall88
closed
3 years ago
7
Build AMR PRG
#66
mbhall88
closed
2 years ago
11
Quantify cluster similarities
#65
mbhall88
closed
3 years ago
25
Visualise clusters
#64
mbhall88
closed
3 years ago
1
Cluster samples based on distances
#63
mbhall88
closed
3 years ago
1
Add minimum FRS filter
#62
mbhall88
closed
3 years ago
10
Investigate mada_1-11 outlier pairs
#61
mbhall88
closed
3 years ago
7
Produce distance matrix from multi-sample VCF
#60
mbhall88
closed
3 years ago
5
Filter multi-sample VCF
#59
mbhall88
closed
3 years ago
4
Normalise multi-sample VCF
#58
mbhall88
closed
3 years ago
3
Combine discovered variants from all samples
#57
mbhall88
closed
3 years ago
1
Perform multi-sample comparison with pandora
#56
mbhall88
closed
3 years ago
0
Mask GFF features for PRG construction
#55
mbhall88
closed
3 years ago
19
Apply variants to loci is missing lots of variants
#54
mbhall88
closed
3 years ago
1
Investigate low recall for pandora variant calls
#53
mbhall88
closed
3 years ago
9
Make VCF reference for PRG
#52
mbhall88
closed
3 years ago
0
Run Illumina data through pandora?
#51
mbhall88
closed
3 years ago
1
Clarify usage of pandora compare
#50
mbhall88
closed
3 years ago
5
Compare pandora calls to truth assemblies
#49
mbhall88
closed
3 years ago
1
Filter pandora map VCFs
#48
mbhall88
closed
3 years ago
16
Normalise pandora map VCFs
#47
mbhall88
closed
3 years ago
0
Call per-sample variants with pandora
#46
mbhall88
closed
3 years ago
7
Index H37Rv PRG
#45
mbhall88
closed
3 years ago
0
Write methods for baseline variant analysis
#44
mbhall88
closed
3 years ago
1
Generate consensus sequence from variant calls
#43
mbhall88
closed
3 years ago
0
Compare variant calls to truth assemblies
#42
mbhall88
closed
3 years ago
5
SNP distance between Illumina and Nanopore calls
#41
mbhall88
closed
3 years ago
9
Investigate concordance outliers
#40
mbhall88
closed
3 years ago
1
Filter nanopore baseline variant calls
#39
mbhall88
closed
3 years ago
23
Concordance of baseline variant callers
#38
mbhall88
closed
3 years ago
15
Add Birmingham data to samplesheet
#37
mbhall88
closed
4 years ago
0
Run Birmingham data through COMPASS
#36
mbhall88
closed
4 years ago
2
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