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sanjaynagi
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AmpSeeker
A snakemake workflow for amplicon sequencing
https://sanjaynagi.github.io/AmpSeeker/
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add aligment QC
#27
eddUG
closed
1 year ago
1
Fastp Implementation
#26
ChabbyTMD
closed
1 year ago
4
Replace TrimFastQs from bbmap to alternative tool
#25
sanjaynagi
closed
1 year ago
2
Pin python version in conda environments
#24
sanjaynagi
closed
1 year ago
1
MultiQC, FastQC and bcftools stats implementation
#23
ChabbyTMD
closed
1 year ago
12
Download previous AgamDao data and evaluate genotyping accuracy
#22
sanjaynagi
closed
6 months ago
6
Search the literature for sensible QC options in Amplicon sequencing
#21
sanjaynagi
closed
1 year ago
3
add multiqc rule to collect qc data
#20
sanjaynagi
closed
1 year ago
1
Bcl Convert Rule
#19
ChabbyTMD
closed
1 year ago
4
Implement allele frequency calculation and visualisation
#18
sanjaynagi
closed
1 year ago
0
Implement principal components analysis
#17
sanjaynagi
closed
1 year ago
0
Build private web page of all results with Jupyter book
#16
sanjaynagi
closed
1 year ago
3
implement bcl to fastq conversion
#15
sanjaynagi
closed
1 year ago
5
igv notebook and renaming
#14
sanjaynagi
closed
1 year ago
8
igv-notebook
#13
sanjaynagi
closed
1 year ago
0
introduce snakemake checkpoint for samples with no data
#12
sanjaynagi
closed
1 year ago
4
Workflow common modifications
#11
ChabbyTMD
closed
1 year ago
3
Common modifications
#10
ChabbyTMD
closed
1 year ago
3
add badges and simplify README
#9
sanjaynagi
closed
1 year ago
1
set standards for bed file, and accompanying tsv file
#8
sanjaynagi
closed
1 year ago
7
Conditional logic 27-10-22
#7
sanjaynagi
closed
1 year ago
2
Implement GitHub actions CI and add test data
#6
sanjaynagi
closed
1 year ago
5
implement github actions CI
#5
sanjaynagi
closed
1 year ago
0
rename the workflow
#4
sanjaynagi
closed
1 year ago
3
move input file list to common.smk
#3
sanjaynagi
closed
1 year ago
8
Conditional Workflow based on Amplicon or Whole Genome Data.
#2
ChabbyTMD
closed
1 year ago
3
Automatic merging of vcf files depending on sample size
#1
sanjaynagi
closed
1 year ago
1
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