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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 support for custom snpeff dbs
#126
sanjaynagi
closed
1 week ago
1
support for custom snpEff db generation
#125
sanjaynagi
closed
1 week ago
0
bug in sample_quality_control
#124
sanjaynagi
opened
3 weeks ago
1
add contributor information to docs
#123
sanjaynagi
opened
3 weeks ago
0
bcl_output should be in results
#122
sanjaynagi
opened
1 month ago
0
Create _toc from _toc_skeleton in process_toc.ipynb
#121
sanjaynagi
closed
1 month ago
1
prevent adding ag-vampir notebooks to _toc.yml if they are present
#120
sanjaynagi
closed
1 month ago
0
update docs and add example sample sheet
#119
sanjaynagi
closed
1 month ago
0
multiallelic sites allele freq calc is wrong
#118
sanjaynagi
closed
4 months ago
1
fixes and improvements
#117
sanjaynagi
closed
4 months ago
0
Implement a run information and run statistics notebook, update ag-vampir.bed
#116
sanjaynagi
closed
4 months ago
0
nb for sample metadata/general run information
#115
sanjaynagi
closed
4 months ago
0
Assign taxon to metadata
#114
sanjaynagi
closed
4 months ago
1
speed up snp-dataframe nb
#113
sanjaynagi
closed
4 months ago
2
Improve allele frequencies
#112
sanjaynagi
closed
4 months ago
2
enable multiple cohort columns
#111
sanjaynagi
closed
4 months ago
1
show frequencies of all ALTs
#110
sanjaynagi
closed
4 months ago
1
update logo
#109
sanjaynagi
closed
4 months ago
0
assign taxon with species id notebook
#108
sanjaynagi
closed
4 months ago
0
a single cohort_columns config option for all analyses
#107
sanjaynagi
closed
4 months ago
1
sample-qc infrastructure
#106
sanjaynagi
closed
4 months ago
0
genetic diversity
#105
sanjaynagi
closed
5 months ago
0
Testing - use whole reference genome from Vectorbase
#104
sanjaynagi
closed
5 months ago
0
testing - replace mini reference with full AgamP4 reference.
#103
sanjaynagi
closed
5 months ago
0
Added kdr origins notebook
#102
EricRLucas
closed
5 months ago
11
primer-rebalancing
#101
sanjaynagi
closed
5 months ago
0
Improve snp-dataframe-excel functions
#100
sanjaynagi
closed
5 months ago
0
update docs
#99
sanjaynagi
opened
6 months ago
0
Diplotype clustering tree of samples
#98
sanjaynagi
opened
6 months ago
1
species-id and ag-vampir/custom panel support
#97
sanjaynagi
closed
6 months ago
1
change colour of sample depth plot
#96
sanjaynagi
closed
4 months ago
1
sample and variant filtering notebook
#95
sanjaynagi
closed
6 months ago
1
add run statistics to home-page
#94
sanjaynagi
closed
4 months ago
3
indels fix + add dsx to targets file
#93
sanjaynagi
closed
7 months ago
0
allow fastq path metadata input
#92
sanjaynagi
closed
7 months ago
0
allow fastq path input in metadata
#91
sanjaynagi
closed
7 months ago
2
read bed file as tabs or spaces
#90
sanjaynagi
closed
4 months ago
1
Make bed input optional
#89
sanjaynagi
opened
10 months ago
1
Diversity analyses
#88
sanjaynagi
closed
5 months ago
0
amplicon x sample read depth table
#87
sanjaynagi
closed
11 months ago
0
amplicon by sample read depth table
#86
sanjaynagi
closed
11 months ago
0
metadata - .xlsx or .csv or .tsv input
#85
sanjaynagi
closed
11 months ago
0
Allow .xlsx for metadata
#84
sanjaynagi
closed
11 months ago
0
move multiqc.yaml to resources/
#83
sanjaynagi
closed
11 months ago
0
Implement snpeff annotation, snp-df nb and process nbs
#82
sanjaynagi
closed
11 months ago
0
add notebook to add 'remove-input' tag to papermill parameter cells
#81
sanjaynagi
closed
11 months ago
0
Implement variant annotation
#80
sanjaynagi
closed
11 months ago
0
Implement gatk
#79
sanjaynagi
closed
11 months ago
1
option to call whole amplicons and move qc analyses to results/qc
#78
sanjaynagi
closed
11 months ago
0
Option to call variants across whole amplicons
#77
sanjaynagi
closed
11 months ago
0
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