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realtimephylogenomics
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lab-strain-resequencing-pipeline
Pipeline for internal lab resequencing projects
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upload test data to AWS and script an MVP analysis
#40
lonelyjoeparker
opened
1 year ago
1
edit the readme.md for this project
#39
lonelyjoeparker
opened
1 year ago
0
Check strains' contamination from validation run
#38
lonelyjoeparker
closed
1 year ago
1
the notification email address in the basecalling and other scripts needs to be notifiable
#37
lonelyjoeparker
closed
1 year ago
3
simplify deployment instructions
#36
lonelyjoeparker
closed
1 year ago
1
Validate and refine SOPs
#35
lonelyjoeparker
closed
1 year ago
3
Validate bioinformatics
#34
lonelyjoeparker
closed
1 year ago
3
Develop a labelling/barcode system
#33
conorg150
opened
2 years ago
2
Review SOP's
#32
conorg150
closed
2 years ago
0
collect all the metadata about the strains
#31
lonelyjoeparker
opened
2 years ago
0
check all the strains are where we think they are
#30
lonelyjoeparker
closed
1 year ago
3
clean up
#29
lonelyjoeparker
closed
1 year ago
0
store and upload assembly
#28
lonelyjoeparker
opened
2 years ago
0
assembly QC
#27
lonelyjoeparker
opened
2 years ago
0
genome assembly
#26
lonelyjoeparker
closed
1 year ago
0
kraken check
#25
lonelyjoeparker
closed
1 year ago
0
demultiplexing - barcoding
#24
lonelyjoeparker
closed
1 year ago
0
basecalling
#23
lonelyjoeparker
closed
1 year ago
0
sequencing
#22
lonelyjoeparker
closed
1 year ago
0
library prep
#21
lonelyjoeparker
closed
1 year ago
0
sample QC
#20
lonelyjoeparker
closed
1 year ago
0
DNA extraction
#19
lonelyjoeparker
closed
1 year ago
0
culture samples
#18
lonelyjoeparker
closed
1 year ago
0
stage samples reagents and kits
#17
lonelyjoeparker
closed
1 year ago
1
conduct validation run
#16
lonelyjoeparker
closed
1 year ago
0
conduct sample triage
#15
lonelyjoeparker
closed
1 year ago
0
verify sample permissions
#14
lonelyjoeparker
opened
2 years ago
4
collect strain accesison info
#13
lonelyjoeparker
opened
2 years ago
1
project washup
#12
lonelyjoeparker
closed
1 year ago
0
train teams
#11
lonelyjoeparker
closed
1 year ago
0
project logistics - allocate work teams
#10
lonelyjoeparker
closed
1 year ago
0
decide operational tasks and owners
#9
lonelyjoeparker
closed
1 year ago
0
design and test resequencing bioinformatics SOPs
#8
lonelyjoeparker
closed
1 year ago
1
Test lab SOPs
#7
lonelyjoeparker
closed
1 year ago
1
Organise logistics - wider stakeholders
#6
lonelyjoeparker
closed
1 year ago
2
Organise logistics - lab space
#5
lonelyjoeparker
closed
1 year ago
3
Get a cost centre code
#4
lonelyjoeparker
closed
2 years ago
2
Procure lab consumables
#3
lonelyjoeparker
closed
1 year ago
6
Collect draft SOPs
#2
lonelyjoeparker
closed
2 years ago
3
Need draft pipeline
#1
lonelyjoeparker
closed
1 year ago
0