nanoplot

fastq

sequencing summary

nanopore

Description

Run NanoPlot on nanopore-sequenced reads.
NanoPlot is a plotting tool for long read sequencing data and alignments.

Type

bash_script

License

MIT

Keywords

fastq

sequencing summary

nanopore

Links

Repository

Documentation

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
outdir: "$id.$key.outdir"  
format: [ "png" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.3.1 \  
  -main-script target/nextflow/nanoplot/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--fastq	file multiple	Input fastq file(s), separated by ";".
--fasta	file multiple	Input fasta file(s), separated by ";".
--fastq_rich	file multiple	Input fastq file(s) generated by albacore or MinKNOW with additional information concerning channel and time, separated by ";".
--fastq_minimal	file multiple	Input fastq file(s) generated by albacore or MinKNOW with additional information concerning channel and time. Minimal data is extracted swiftly without elaborate checks. Separated by ";".
--summary	file multiple	Input summary file(s) generated by albacore or guppy, separated by ";".
--bam	file multiple	Input sorted bam file(s), separated by ";".
--ubam	file multiple	Input unmapped bam file(s), separated by ";".
--cram	file multiple	Input sorted cram file(s), separated by ";".
--pickle	file multiple	Input pickle file stored earlier, separated by ";".
--feather --arrow	file multiple	Input feather file(s), separated by ";".

Name

Type & Properties

--fastq

file

multiple

--fasta

file

multiple

--fastq_rich

file

multiple

--fastq_minimal

file

multiple

--summary

file

multiple

--bam

file

multiple

--ubam

file

multiple

--cram

file

multiple

--pickle

file

multiple

--feather

--arrow

file

multiple

Outputs

Name	Type & Properties	Description
--outdir -o	file required output	Specify directory in which output has to be created.

Name

Type & Properties

--outdir

-o

file

required

output

Options

Name	Type & Properties	Description
--verbose	boolean_true	Write log messages also to terminal
--store	boolean_true	Store the extracted data in a pickle file for future plotting.
--raw	boolean_true	Store the extracted data in tab separated file.
--huge	boolean_true	Input data is one very large file.
--no_static	boolean_false	Do not make static (png) plots.
--prefix -p	string	Specify an optional prefix to be used for the output files.
--tsv_stats	boolean_true	Output the stats file as a properly formatted TSV.
--only_report	boolean_true	Output only the report.
--info_in_report	boolean_true	Add NanoPlot run info in the report.

Name

Type & Properties

--verbose

boolean_true

--store

boolean_true

--raw

boolean_true

--huge

boolean_true

--no_static

boolean_false

--prefix

-p

string

--tsv_stats

boolean_true

--only_report

boolean_true

--info_in_report

boolean_true

Filtering or transforming input

Name	Type & Properties	Description
--maxlength	integer	Drop reads longer than length specified.
--minlength	integer	Drop reads shorter than length specified.
--drop_outliers	boolean_false	Drop outlier reads with extreme long length.
--downsample	integer	Reduce dataset to N reads by random sampling.
--loglength	boolean_true	Logarithmic scaling of lengths in plots.
--percentqual	boolean_true	Use qualities as theoretical percent identities.
--alength	boolean_true	Use aligned read lengths rather than sequenced length (bam mode).
--minqual	integer	Drop reads with an average quality lower than specified.
--runtime_until	integer	Only take the N first hours of a run.
--readtype	string	Which read type to extract information about from summary. Options are 1D, 2D, 1D2
--barcoded	boolean_true	Use if you want to split the summary file by barcode.
--no_supplementary	boolean_false	Use if you want to remove supplementary alignments.

Name

Type & Properties

--maxlength

integer

--minlength

integer

--drop_outliers

boolean_false

--downsample

integer

--loglength

boolean_true

--percentqual

boolean_true

--alength

boolean_true

--minqual

integer

--runtime_until

integer

--readtype

string

--barcoded

boolean_true

--no_supplementary

boolean_false

Customizing plots

Name	Type & Properties	Description
--color -c	string	Specify a color for the plots, must be a valid matplotlib color.
--colormap -cm	string	Specify a valid matplotlib colormap for the heatmap.
--format -f	string	Specify the output format of the plots. {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}
--plots	string	Specify which bivariate plots have to be made. [{kde,hex,dot} ...]
--legacy	string	Specify which bivariate plots have to be made (legacy mode). [{kde,dot,hex} ...]
--listcolors	boolean_true	List the colors which are available for plotting and exit.
--listcolormaps	boolean_true	List the colormaps which are available for plotting and exit.
--no_N50	boolean_false	Hide the N50 mark in the read length histogram.
--N50	boolean_true	Show the N50 mark in the read length histogram.
--title	string	Add a title to all plots, requires quoting if using spaces.
--font_scale	double	Scale the font of the plots by a factor.
--dpi	integer	Set the dpi for saving images.
--hide_stats	boolean_false	Not adding Pearson R stats in some bivariate plots.

Name

Type & Properties

--color

-c

string

--colormap

-cm

string

--format

-f

string

--plots

string

--legacy

string

--listcolors

boolean_true

--listcolormaps

boolean_true

--no_N50

boolean_false

--N50

boolean_true

--title

string

--font_scale

double

--dpi

integer

--hide_stats

boolean_false