blobtools

blobtools subworkflow

Blobtools is a useful tool for identification of possible inter-species contamination. The blobtools subworkflow is an optional workflow that requires a blast databases. Instructions on how to download a blast database can be found on a different wiki page.

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blobtools subworkflow
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flowchart LR
fastq --> bbmap
contigs --> bbmap
contigs --> blastn
bbmap --> create
blastn --> create
create --> view
create --> plot

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Relevant params with their default values:

params.blast_db                   = "/path/to/blast_db/directory"
params.bbmap_options              = ""
params.blast_db_type              = "nt"
params.blastn_options             = "-max_target_seqs 10 -max_hsps 1 -evalue 1e-25"
params.blobtools_create_options   = ""
params.blobtools_view_options     = ""
params.blobtools_plot_options     = "--format png -r species"
params.blobtools_bbmap_options    = ""