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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.
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Run Birmingham data through QC pipeline
#35
mbhall88
closed
4 years ago
0
Rsync Birmingham data to NFS and FTP
#34
mbhall88
closed
4 years ago
0
Move Birmingham Illumina data to project directory
#33
mbhall88
closed
4 years ago
1
Demultiplex Birmingham nanopore data
#32
mbhall88
closed
4 years ago
0
Basecall Birmingham nanopore data
#31
mbhall88
closed
4 years ago
0
Convert single-fast5 to multi-fast5
#30
mbhall88
closed
4 years ago
2
Write methods for QC
#29
mbhall88
closed
3 years ago
2
Organise PHE Birmingham data
#28
mbhall88
closed
4 years ago
1
Produce QC report
#27
mbhall88
closed
4 years ago
1
Assign lineages for project samples
#26
mbhall88
closed
4 years ago
3
Decontamination of reads
#25
mbhall88
closed
4 years ago
3
Maximum coverage threshold for samples
#24
mbhall88
closed
4 years ago
3
Excluding samples based on coverage
#23
mbhall88
closed
4 years ago
7
Quality control
#22
mbhall88
closed
4 years ago
1
Write methods for AMR PRG construction
#21
mbhall88
closed
3 years ago
1
Write Paper
#20
mbhall88
closed
2 years ago
0
Convert COMPASS gVCFs to VCFs
#19
mbhall88
closed
4 years ago
2
Run baseline variant calling for nanopore data
#18
mbhall88
closed
4 years ago
7
Run COMPASS on Illumina data
#17
mbhall88
closed
4 years ago
3
Build local PRGs
#16
mbhall88
closed
4 years ago
1
Multiple sequence alignment of "founder" variants
#15
mbhall88
closed
4 years ago
2
Subsample PRG "founder" variants
#14
mbhall88
closed
4 years ago
4
Project-wide genome mask
#13
mbhall88
closed
4 years ago
1
Lineage-specific VCFs
#12
mbhall88
closed
4 years ago
1
Assign lineages
#11
mbhall88
closed
4 years ago
15
Apply variants to H37Rv reference chunks
#10
mbhall88
closed
3 years ago
10
Split H37Rv based on annotation
#9
mbhall88
closed
4 years ago
7
Drug susceptibility prediction
#8
mbhall88
closed
2 years ago
0
Reproducing "truth" Illumina clusters using genome graphs and nanopore
#7
mbhall88
closed
3 years ago
17
Basic analysis of per-sample variant calls
#6
mbhall88
closed
3 years ago
0
Variant caller to use for baseline analysis
#5
mbhall88
closed
4 years ago
1
Baseline variant analysis
#4
mbhall88
closed
4 years ago
0
Construct PRGs
#3
mbhall88
closed
3 years ago
1
Use FORGe to rank variants
#2
mbhall88
closed
4 years ago
8
Evaluate basecalling model
#1
mbhall88
closed
4 years ago
3
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