Description

A derivative of GenomeScope2.0 modified to work with FastK

Input

Name (Type)
Description
Pattern

meta (map)

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

]

fastk_histex_histogram (file)

A histogram formatted for GeneScope using the -G parameter from Fastk Histex

*.hist

Output

Name (Type)
Description
Pattern

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

linear_plot (file)

A GeneScope linear plot in PNG format

*_linear_plot.png

transformed_linear_plot (file)

A GeneScope transformed linear plot in PNG format

*_transformed_linear_plot.png

log_plot (file)

A GeneScope log plot in PNG format

*_log_plot.png

transformed_log_plot (file)

A GeneScope transformed log plot in PNG format

*_transformed_log_plot.png

model (file)

GeneScope model fit summary

*_model.txt

summary (file)

GeneScope histogram summary

*_summary.txt

kmer_cov (float)

Average kmer coverage value extracted from summary file

[0-9.]+
included in
genomeassembler
maintainer
Github user mahesh-panchal
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

genescopefk
https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE

A derivative of GenomeScope2.0 modified to work with FastK

github.com/thegenemyers/GENESCOPE.FK https://github.com/thegenemyers/GENESCOPE.FK