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sanjaynagi
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AmpSeeker
A state-of-the-art snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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add empty reads/references folders, and welcome message
#76
sanjaynagi
closed
11 months ago
0
empty read and reference folder with .gitignore
#75
sanjaynagi
closed
11 months ago
0
STDOUT message upon running pipeline
#74
sanjaynagi
closed
11 months ago
0
MultiQC Fastp and Qualimap results intergration.
#73
ChabbyTMD
closed
12 months ago
4
change all plotly plots to white background
#72
sanjaynagi
closed
12 months ago
1
Individual level SNP table
#71
sanjaynagi
closed
11 months ago
0
Fix for childioexception error
#70
ChabbyTMD
closed
12 months ago
5
BCL Conversion Failing.
#69
ChabbyTMD
closed
12 months ago
5
bwa index outputs explicit!
#68
sanjaynagi
closed
1 year ago
1
make bwa index output files explicit
#67
sanjaynagi
closed
1 year ago
1
CI does not test starting from Illumina BCL folder
#66
sanjaynagi
opened
1 year ago
0
Quality control notebooks
#65
sanjaynagi
closed
1 year ago
2
add links to fastp and fastqc htmls within AmpSeeker results book
#64
sanjaynagi
closed
1 year ago
2
improve coverage nb
#63
sanjaynagi
closed
1 year ago
0
coverage by sample
#62
sanjaynagi
closed
1 year ago
0
Index read quality
#61
sanjaynagi
closed
1 year ago
0
add rev comp notebook
#60
sanjaynagi
closed
1 year ago
1
signularity bcl-convert
#59
sanjaynagi
closed
1 year ago
0
bcl convert not available through conda
#58
sanjaynagi
closed
1 year ago
1
fix logo
#57
sanjaynagi
closed
6 months ago
1
IGV notebook not working in results book
#56
sanjaynagi
closed
6 months ago
1
Suggestions for input files page
#55
ChabbyTMD
closed
1 year ago
1
Implement allele frequencies notebook
#54
sanjaynagi
closed
1 year ago
0
Dynamically generate toc.yaml
#53
sanjaynagi
closed
11 months ago
2
add public documentation
#52
sanjaynagi
closed
1 year ago
2
Fix the Ampseeker-results book figures
#51
sanjaynagi
closed
1 year ago
1
move result book from docs/ to results/
#50
sanjaynagi
closed
1 year ago
0
Assess index read quality
#49
sanjaynagi
closed
1 year ago
0
Fix jupyter results book plots not showing
#48
sanjaynagi
closed
1 year ago
0
robust renaming using bcl convert file mapping
#47
sanjaynagi
closed
1 year ago
1
rename samples after demultiplexing in more robust way
#46
sanjaynagi
closed
1 year ago
1
remove-inputs and add option for pca colour column
#45
sanjaynagi
closed
1 year ago
0
Heatmap of reads per well
#44
sanjaynagi
closed
1 year ago
3
Make all analyses optional in the config.yaml
#43
ChabbyTMD
closed
1 year ago
3
Make tutorial video
#42
sanjaynagi
opened
1 year ago
0
Interactive sample map
#41
sanjaynagi
closed
1 year ago
0
remove intro bits in results-book
#40
sanjaynagi
closed
1 year ago
1
Add interactive sample map
#39
sanjaynagi
closed
1 year ago
0
AgamDao modules
#38
sanjaynagi
closed
5 months ago
3
implement principal components analysis notebook
#37
sanjaynagi
closed
1 year ago
0
Qualimap wrapper error
#36
sanjaynagi
closed
1 year ago
3
Make documentation webpage
#35
sanjaynagi
closed
1 year ago
3
Coverage notebook
#34
sanjaynagi
closed
1 year ago
5
create symlink to jupyter-book which is stored in main workflow directory
#33
sanjaynagi
closed
1 year ago
0
Make all analyses optional
#32
sanjaynagi
closed
1 year ago
2
Private webpage 24 04 23
#31
ChabbyTMD
closed
1 year ago
4
Implement coverage notebook
#30
sanjaynagi
closed
1 year ago
0
Make a logo
#29
sanjaynagi
closed
1 year ago
1
add quality control steps post variant-calling
#28
sanjaynagi
closed
5 months ago
3
add aligment QC
#27
eddUG
closed
1 year ago
1
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