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In order to complete tombo analysis, the raw signal and associated canonical basecalls are required. These basecalls are produced from the raw signal either during the run by minknow or post-analysis by the guppy software.
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Re-squiggle Algorithm — Tombo 1.5.1 documentation - GitHub Pages
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tombo package — Tombo 1.5.1 documentation - GitHub Pages
Plot Region Selection. Most Tombo plotting functions are genome-anchored. These commands create plots analogous to a genome browser, but including all raw signal within a region. The available commands differ in their mode of genome region selection. This allows users to plot regions of interest for many research contexts.
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Check --basecall-group '+'option if basecalls are stored in non-standard location or '+'use `tombo preprocess annotate_raw_with_fastqs` to add '+'basecalls from FASTQ files to raw FAST5 files.')returnfiles,fast5s_basedir,lock_fnsdef_resquiggle_main(args):"""Main method for resquiggle """ifargs.processes>1and_DEBUG_PLOTTING:th.error_message_and ...
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"Reads do not contain basecalls" error. · Issue #205 · nanoporetech/tombo
The --corrected-group slot contains attributes for the signal normalization (shift, scale, upper_limit, lower_limit, outlier_threshold and the tombo signal matching score) as well as a boolean flag indicating whether the read is DNA or RNA.
tombo resquiggle · Issue #5 · nanoporetech/tombo · GitHub
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