modules/genomescope2

Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach

genome sizegenome heterozygosityrepeat content

https://github.com/nf-core/modules/[...]/modules/nf-core/genomescope2

Description

Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`histogram:file`

A K-mer histogram file

*.hist

Output

name:type

description

pattern

`linear_plot_png`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_linear_plot.png:file`

A genomescope2 linear plot in PNG format

*_linear_plot.png

`transformed_linear_plot_png`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_transformed_linear_plot.png:file`

A genomescope2 transformed linear plot in PNG format

*_transformed_linear_plot.png

`log_plot_png`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_log_plot.png:file`

A genomescope2 log plot in PNG format

*_log_plot.png

`transformed_log_plot_png`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_transformed_log_plot.png:file`

A genomescope2 transformed log plot in PNG format

*_transformed_log_plot.png

`model`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_model.txt:file`

Genomescope2 model fit summary

*_model.txt

`summary`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_summary.txt:file`

Genomescope2 histogram summary

*_summary.txt

`lookup_table`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_lookup_table.txt:file`

Fitted histogram lookup table

*_lookup_table.txt

`fitted_histogram_png`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end

]

`${prefix}_fitted_hist.png:file`

A genomescope2 fitted histogram plot in PNG format

*_fitted_hist.png

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

genomescope2
Apache-2.0

Reference-free profiling of polyploid genomes

http://qb.cshl.edu/genomescope/genomescope2.0 github.com/tbenavi1/genomescope2.0/blob/master/README.md https://github.com/tbenavi1/genomescope2.0 10.1038/s41467-020-14998-3

modules/genomescope2

Description

Input

`meta:map`

`histogram:file`

Output

`linear_plot_png`

`meta:map`

`${prefix}_linear_plot.png:file`

`transformed_linear_plot_png`

`meta:map`

`${prefix}_transformed_linear_plot.png:file`

`log_plot_png`

`meta:map`

`${prefix}_log_plot.png:file`

`transformed_log_plot_png`

`meta:map`

`${prefix}_transformed_log_plot.png:file`

`model`

`meta:map`

`${prefix}_model.txt:file`

`summary`

`meta:map`

`${prefix}_summary.txt:file`

`lookup_table`

`meta:map`

`${prefix}_lookup_table.txt:file`

`fitted_histogram_png`

`meta:map`

`${prefix}_fitted_hist.png:file`

`versions`

`versions.yml:file`

Tools

genomescope2
Apache-2.0

included in

maintainer

get in touch

modules/genomescope2

Description

Input

meta:map

histogram:file

Output

linear_plot_png

meta:map

${prefix}_linear_plot.png:file

transformed_linear_plot_png

meta:map

${prefix}_transformed_linear_plot.png:file

log_plot_png

meta:map

${prefix}_log_plot.png:file

transformed_log_plot_png

meta:map

${prefix}_transformed_log_plot.png:file

model

meta:map

${prefix}_model.txt:file

summary

meta:map

${prefix}_summary.txt:file

lookup_table

meta:map

${prefix}_lookup_table.txt:file

fitted_histogram_png

meta:map

${prefix}_fitted_hist.png:file

versions

versions.yml:file

Tools

genomescope2 Apache-2.0

included in

maintainer

get in touch

`meta:map`

`histogram:file`

`linear_plot_png`

`meta:map`

`${prefix}_linear_plot.png:file`

`transformed_linear_plot_png`

`meta:map`

`${prefix}_transformed_linear_plot.png:file`

`log_plot_png`

`meta:map`

`${prefix}_log_plot.png:file`

`transformed_log_plot_png`

`meta:map`

`${prefix}_transformed_log_plot.png:file`

`model`

`meta:map`

`${prefix}_model.txt:file`

`summary`

`meta:map`

`${prefix}_summary.txt:file`

`lookup_table`

`meta:map`

`${prefix}_lookup_table.txt:file`

`fitted_histogram_png`

`meta:map`

`${prefix}_fitted_hist.png:file`

`versions`

`versions.yml:file`

genomescope2
Apache-2.0