What it does

To visualize, quality control and taxonomic partitioning of genome datasets. Blobtools plot is used to produce two coverage plot in png format and a statistic file.

Input

• Blob file - a Blob json file.

Parameters

• infile - BlobDB file (created with "blobtools create")
• lib - Plot only certain covlib(s). Separated by ","
• notitle - Do not add filename as title to plot
• filelabel - Label axis based on filenames
• plotgroups INT - Number of (taxonomic) groups to plot, remaining groups are placed in 'other' [default: 8]
• length INT - Minimum sequence length considered for plotting [default: 100]
• cindex - Colour blobs by 'c index' [default: False]
• nohit - Hide sequences without taxonomic annotation [default: False]
• noscale - Do not scale sequences by length [default: False]
• legend - Plot legend of blobplot in separate figure
• multiplot - Multi-plot. Print blobplot for each (taxonomic) group separately
• cumulative - Print plot after addition of each (taxonomic) group
• sort <ORDER> - Sort order for plotting [default: span] 1) span : plot with decreasing span 2) count : plot with decreasing count
• hist <HIST> - Data for histograms [default: span] 1) span : span-weighted histograms 2) count : count histograms
• rank <RANK> - Taxonomic rank used for colouring of blobs [default: phylum] (Supported: species, genus, family, order,phylum, superkingdom)
• taxrule <TAXRULE> - Taxrule which has been used for computing taxonomy (Supported: bestsum, bestsumorder) [default: bestsum]
• format FORMAT - Figure format for plot (png, pdf, eps, jpeg,ps, svg, svgz, tiff) [default: png]
• label GROUPS - Relabel (taxonomic) groups, can be used several times. e.g. "A=Actinobacteria,Proteobacteria
• colours COLOURFILE - File containing colours for (taxonomic) groups. This allows having more than 9 colours.
• exclude GROUPS - Exclude these (taxonomic) groups (also works for 'other') e.g. "Actinobacteria,Proteobacteria,other"
• refcov <FILE> - File containing number of "total" and "mapped" reads per coverage file. (e.g.: bam0,900,100). If provided, info will be used in read coverage plot(s).

-catcolour <FILE> - Colour plot based on categories from FILE (format : "seq category").

Command line Example:

• blobtools plot -i example_blobDB.json -o output_file_preifix

Output

• Coverage PNG file
• Read Coverage PNG file
• Statistic file

Contributor

Galaxy Australia wrapped the Blobtools: the original software is available in this Github repository.

References