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  1. TOMBO - Download Site - TOMBO

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    DOI: 10.1016/j.cpc.2014.11.012 This document explains detail algorithms of the all-electron mixed basis approach and TOMBO program. This is the latest version (2024 ver. 1) of TOMBO manual. This PDF tutorial textbook explains Examples for beginners.
    User-created Tombo models can be used in re-squiggling, modified base detection and plotting commands using the advanced --tombo-model-filename option. This option is generally for advanced users training their own models, so this option is not shown in the command line help documentation, but is available for all applicable commands.
    Tombo is available for installation via pip, but requires an R installation as well as R package dependencies (ggplot2 and gridextra) for all visualization functions. Tombo can also be installed directly from source (mostly for development) by running the following commands: pip install -e .
    Official Tombo python API release ( documentation here) This release also includes various bug fixes including a change to the statistics file allowing processing of arbitrarily large genomes.
  3. Tombo Tutorials — Tombo 1.5.1 documentation

    WebTombo Tutorials. View page source. Tombo Tutorials ¶. This page contains several tutorials with commands to perform suggested Tombo analysis pipelines. Human CpG Methylation Detection. De novo Bacterial …

  4. Model Training (Advanced Users Only) — Tombo 1.5.1 …

    WebModel training produces a binary Tombo model file (as those packaged with Tombo found in the code repository in tombo/tombo_models). User-created Tombo models can be used in re-squiggling, modified base detection …

  5. Modified Base Detection — Tombo 1.5.1 …

    WebTombo enables four methods (including two sample comparison methods) for detecting shifts in raw current signal level, indicative of non-canonical bases. These four methods allow researchers to investigate non …

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