Metadata-Version: 1.0
Name: ont-tombo
Version: 1.0
Summary: Analysis of raw nanopore sequencing data.
Home-page: https://github.com/nanoporetech/tombo
Author: Marcus Stoiber
Author-email: marcus.stoiber@nanoporetech.com
License: mpl-2.0
Description-Content-Type: UNKNOWN
Description: =======
        Summary
        =======
        
        Tombo is a suite of tools primarily for the identification of modified
        nucleotides from nanopore sequencing data. Tombo also provides tools for
        the analysis and visualization of raw nanopore signal.
        
        ============
        Installation
        ============
        
        Basic tombo installation
        
        ::
        
            # install via conda environment
            conda install ont-tombo
        
            # or install pip package (numpy install required before tombo for cython optimization)
            pip install numpy
            pip install ont-tombo
        
        ..
        
            Additional installation instructions options
        
        =========
        Use Cases
        =========
        
        Perform re-squiggle algorithm (once per root directory of FAST5 files)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        \* Need not contain Events data, but must contain Fastq slot
        
        ::
        
            tombo resquiggle path/to/amplified/dna/fast5s/ genome.fasta --minimap2-executable ./minimap2 --processes 4
        
        Identify modified nucleotides comparing to an alternative 5mC model
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo test_significance --fast5-basedirs path/to/native/dna/fast5s/ --alternate-bases 5mC --statistics-file-basename sample_compare
            tombo write_wiggles --fast5-basedirs path/to/native/dna/fast5s/ --wiggle-basename sample_compare.5mC --statistics-filename sample_compare.5mC.tombo.stats
        
        Identify modified nucleotides from a single sample
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo test_significance --fast5-basedirs path/to/native/dna/fast5s/ --statistics-file-basename sample --processes 4
            tombo write_wiggles --fast5-basedirs path/to/native/dna/fast5s/ --wiggle-basename sample --statistics-filename sample.tombo.stats
        
        Identify modified nucleotides comparing two samples
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo test_significance --fast5-basedirs path/to/native/dna/fast5s/ --control-fast5-basedirs path/to/amplified/dna/fast5s/  --statistics-file-basename sample_compare
            tombo write_wiggles --fast5-basedirs path/to/native/dna/fast5s/ --control-fast5-basedirs path/to/amplified/dna/fast5s/ --wiggle-basename sample_compare --statistics-filename sample_compare.tombo.stats
        
        Identify modified RNA nucleotides from a single sample
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo resquiggle path/to/native/rna/fast5s/ transcriptome.fasta --minimap2-executable ./minimap2 --processes 4
            tombo test_significance --fast5-basedirs path/to/native/rna/fast5s/ --statistics-file-basename rna_sample --processes 4
            tombo write_wiggles --fast5-basedirs path/to/native/rna/fast5s/ --wiggle-basename rna_sample --statistics-filename rna_sample.tombo.stats
        
        Some plotting examples
        ^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo plot_max_coverage --fast5-basedirs path/to/native/rna/fast5s/ --tombo-model-filename /path/to/tombo/root/tombo/tombo_models/tombo.DNA.model
            tombo plot_motif_centered --fast5-basedirs path/to/native/rna/fast5s/ --motif AWC --genome-fasta genome.fasta --control-fast5-basedirs path/to/amplified/dna/fast5s/ --deepest-coverage
            tombo plot_per_read --fast5-basedirs path/to/native/rna/fast5s/ --genome-locations chromosome:1000 chromosome:2000:- --alternate-model-filename /path/to/tombo/root/tombo/tombo_models/tombo.DNA.5mC.model
        
        Extract sequences surrounding modified positions
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
            tombo write_most_significant_fasta --statistics-filename sample_compare.5mC.tombo.stats --genome-fasta genome.fasta
        
        =====
        Usage
        =====
        
        ::
        
            tombo -h
            tombo [command] [options]
        
        Resquiggle (Must be run before any other commands):
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             resquiggle                    Re-annotate raw signal with genomic aignement of existing basecalls.
        
        Statistical Testing Command:
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             test_significance             Test for shifts in signal against a reference or against another set of reads.
        
        Text Output Commands:
        ^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             write_wiggles                 Write wiggle files for nanopore signal values, coverage, and statistics.
             write_most_significant_fasta  Write sequence where signal differs the most significantly between two groups.
        
        Genome Anchored Plotting Commands:
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             plot_max_coverage             Plot signal in regions with maximal coverage.
             plot_genome_location          Plot signal at defined genomic locations.
             plot_motif_centered           Plot locations centered on a specific motif.
             plot_max_difference           Plot locations where signal differs the most between two groups.
             plot_most_significant         Plot locations where signal differs most significantly between two groups.
             plot_model_most_significant   Plot locations where signal differs most significantly from the kmer model.
             plot_motif_with_stats         Plot signal from several regions and test statistics centered on a k-mer of interst.
             plot_per_read                 Plot per read modified base predictions.
        
        Sequencing Time Anchored Plotting Commands:
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             plot_correction               Plot segmentation before and after correction.
             plot_multi_correction         Plot multiple raw signals anchored by genomic location.
        
        Other Plotting Commands:
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             cluster_most_significant      Clustering traces at bases with significant differences.
             plot_kmer                     Plot signal quantiles acorss kmers.
        
        Read Filtering (Only effects tombo index file):
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             clear_filters                 Clear filters to process all successfully re-squiggled reads.
             filter_stuck                  Apply filter based on observations per base thresholds.
        
        Event-based Re-squiggle (Primarily for producing new models):
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        ::
        
             event_resquiggle              Re-annotate raw signal with genomic alignment from existing basecalls.
             model_resquiggle              Re-annotate raw signal with genomic bases by shifting the signal to more closely match a k-mer model.
             estimate_kmer_reference       Estimate reference k-mer model derived from the provided reads.
             estimate_alt_reference        Estimate alternative tombo model from a sample containing standard bases spiked with a single non-standard base at random positions.
        
        ..
        
            Get additional help for subcommands with ``tombo [command] -h``
        
        ============
        Requirements
        ============
        
        At least one supported mapper:
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  minimap2 (https://github.com/lh3/minimap2)
        -  BWA-MEM (http://bio-bwa.sourceforge.net/)
        -  graphmap (https://github.com/isovic/graphmap)
        
        -  HDF5 (http://micro.stanford.edu/wiki/Install_HDF5#Install)
        
        python Requirements (handled by pip):
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  numpy (must be installed before installing tombo)
        -  scipy
        -  h5py
        -  cython
        
        Optional packages for plotting (install R packages with ``install.packages([package_name])`` from an R prompt):
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  rpy2 (along with an R installation)
        -  ggplot2 (required for any plotting subcommands)
        -  cowplot (required for plot_motif_with_stats subcommand)
        
        Optional packages for alternative model estimation:
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        -  sklearn
        
        Installation along with additional dependencies
        -----------------------------------------------
        
        Install tombo with all optional dependencies (for plotting and model
        estimation)
        
        ::
        
            pip install ont-tombo[full]
        
        Install tombo with plotting dependencies (requires separate installation
        of R packages ggplot2 and cowplot)
        
        ::
        
            pip install ont-tombo[plot]
        
        Install tombo with alternative model estimation dependencies
        
        ::
        
            pip install ont-tombo[alt_est]
        
        Install github version of tombo (most versions on pypi should be up-to-date)
        
        ::
        
            pip install git+https://github.com/nanoporetech/tombo.git
        
        ========
        Citation
        ========
        
        Stoiber, M.H. et al. De novo Identification of DNA Modifications Enabled
        by Genome-Guided Nanopore Signal Processing. bioRxiv (2016).
        
        http://biorxiv.org/content/early/2017/04/10/094672
        
Keywords: nanopore high-throughput sequencing correction genome
Platform: UNKNOWN
