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Arcadia-Science
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2022-prjna853785-sourmash
snakemake pipeline to analyze assemblies from a subset of run accessions in prjna853785 cheese production samples
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notebook updates after running on single sample, wh
#17
taylorreiter
opened
1 year ago
0
Refactor sourmash database download
#16
taylorreiter
closed
1 year ago
0
add a pavian plot
#15
taylorreiter
opened
1 year ago
0
rarefaction/species accumulation curves
#14
taylorreiter
closed
1 year ago
2
there might be a cheese-specific fungi database
#13
taylorreiter
opened
1 year ago
0
add a bar chart of genome size and fraction of genome decteded in sample
#12
taylorreiter
opened
1 year ago
1
filter based on confidence
#11
taylorreiter
closed
1 year ago
1
for heatmap visualization, allow viz for subsets of genomes of interest
#10
taylorreiter
opened
1 year ago
0
for strain plots, considering refactoring code so that each species has it's own color legend instead of all strains for all species
#9
taylorreiter
closed
1 year ago
1
Initial visualization notebooks for sourmash outputs
#8
taylorreiter
closed
1 year ago
1
consider adding co-occurrence analysis
#7
taylorreiter
closed
1 year ago
1
need to add a viz env
#6
taylorreiter
opened
2 years ago
0
Standardize `Snakefile` to match `viral.snakefile` and to accomodate new files
#5
taylorreiter
opened
2 years ago
1
consider adding the checkV database into gather results
#4
taylorreiter
opened
2 years ago
1
upload sourmash output files and binderize this repository
#3
taylorreiter
opened
2 years ago
0
checklist of visualizations to add
#2
taylorreiter
opened
2 years ago
0
Start project with readme, environment, and itial snakemake workflow to execute sourmash commands
#1
taylorreiter
closed
2 years ago
2