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wdecoster / NanoPlot

Plotting scripts for long read sequencing data
http://nanoplot.bioinf.be
MIT License
413 stars 47 forks source link

bonito support #230

Closed aspitaleri closed 3 years ago

aspitaleri commented 3 years ago

Hi still great ever tool! Do you plan to support bonito summary tsv output from basecalling?

wdecoster commented 3 years ago

I have no idea how that looks like, if you can share an example I can have a look.

aspitaleri commented 3 years ago

the output is a tsv like this:

filename    read_id run_id  channel mux start_time  duration    template_start  template_duration   sequence_length_template    mean_qscore_template
FAF17394_44855949_94.fast5  0017323b-af02-4832-afdb-3a91ae540b4d    44855949b830beb3a211cf87665ad44976228ba3    147 1   65109.156   31.903  65109.156   31.903  5910    0.0
wdecoster commented 3 years ago

That looks a lot like a guppy summary file, but I guess you tested already if NanoPlot works with the bonito summary?

aspitaleri commented 3 years ago

actually I didn't yet. I will.

aspitaleri commented 3 years ago

NanoPlot --summary basecalls_summary.tsv.gz -o summary-plots-log --loglength --N50 it worked as a charm!

wdecoster commented 3 years ago

Good to hear.