Nanopore

Owned by Dena Leshkowitz
Last updated: 01 May, 2022 by Ester Feldmesser
3 min read

Collection of Tools: 

ONT - NANOPORE APPLICATION TOOLS

[vitalyg@cn100 ~]$ module load python/bio-2.7.13 

[vitalyg@cn100 ~]$ python

Python 2.7.13 (default, May 14 2017, 14:06:55) 

[GCC 4.8.5 20150623 (Red Hat 4.8.5-11)] on linux2

Type "help", "copyright", "credits" or "license" for more information.

>>> import wub

>>> help(wub)

>>> Help on package wub:                                     


NAME                                                     

    wub - # -*- coding: utf-8 -*-                        


FILE                                                     

    /apps/RH7U2/gnu/python/bio-2.7.13/lib/python2.7/site-packages/Wub-0.2.0-py2.7.egg/wub/__init__.py              


PACKAGE CONTENTS                                         

    bam (package)                                        

    mappers (package)

    parsers (package)

    read_stats (package)

    simulate (package)

    tests (package)

    util (package)

    vis (package)

    wrappers (package)


DATA

    __author__ = 'ONT Applications Group'

    __email__ = 'Apps@nanoporetech.com'

    __version__ = '0.2.0'

Spades

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. http://spades.bioinf.spbau.ru/release3.9.0/manual.html




NanoPlot

[vitalyg@bio ~]$ module load python/3.6.3
[vitalyg@bio ~]$ NanoPlot -h   
usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw]
                [-o OUTDIR] [-p PREFIX] [--maxlength N] [--minlength N]
                [--drop_outliers] [--downsample N] [--loglength]
                [--percentqual] [--alength] [--minqual N] [--runtime_until N]
                [--readtype {1D,2D,1D2}] [--barcoded] [-c COLOR]
                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]
                [--plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]]
                [--listcolors] [--no-N50] [--N50] [--title TITLE]
                (--fastq file [file ...] | --fasta file [file ...] | --fastq_rich file [file ...] | --fastq_minimal file [file ...] | --summary file [file ...] | --bam file [file ...] | --cram file [file ...] | --pickle pickle)

CREATES VARIOUS PLOTS FOR LONG READ SEQUENCING DATA.

General options:
  -h, --help            show the help and exit
  -v, --version         Print version and exit.
  -t, --threads THREADS
                        Set the allowed number of threads to be used by the script
  --verbose             Write log messages also to terminal.
  --store               Store the extracted data in a pickle file for future plotting.
  --raw                 Store the extracted data in tab separated file.
  -o, --outdir OUTDIR   Specify directory in which output has to be created.
  -p, --prefix PREFIX   Specify an optional prefix to be used for the output files.

Options for filtering or transforming input prior to plotting:
  --maxlength N         Drop reads longer than length specified.
  --minlength N         Drop reads shorter than length specified.
  --drop_outliers       Drop outlier reads with extreme long length.
  --downsample N        Reduce dataset to N reads by random sampling.
  --loglength           Logarithmic scaling of lengths in plots.
  --percentqual         Use qualities as theoretical percent identities.
  --alength             Use aligned read lengths rather than sequenced length (bam mode)
  --minqual N           Drop reads with an average quality lower than specified.
  --runtime_until N     Only take the N first hours of a run
  --readtype {1D,2D,1D2}
                        Which read type to extract information about from summary. Options are 1D, 2D,
                        1D2
  --barcoded            Use if you want to split the summary file by barcode

Options for customizing the plots created:
  -c, --color COLOR     Specify a color for the plots, must be a valid matplotlib color
  -f, --format {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}
                        Specify the output format of the plots.
  --plots [{kde,hex,dot,pauvre} [{kde,hex,dot,pauvre} ...]]
                        Specify which bivariate plots have to be made.
  --listcolors          List the colors which are available for plotting and exit.
  --no-N50              Hide the N50 mark in the read length histogram
  --N50                 Show the N50 mark in the read length histogram
  --title TITLE         Add a title to all plots, requires quoting if using spaces

Input data sources, one of these is required.:
  --fastq file [file ...]
                        Data is in one or more default fastq file(s).
  --fasta file [file ...]
                        Data is in one or more fasta file(s).
  --fastq_rich file [file ...]
                        Data is in one or more fastq file(s) generated by albacore or MinKNOW with
                        additional information concerning channel and time.
  --fastq_minimal file [file ...]
                        Data is in one or more fastq file(s) generated by albacore or MinKNOW with
                        additional information concerning channel and time. Minimal data is extracted
                        swiftly without elaborate checks.
  --summary file [file ...]
                        Data is in one or more summary file(s) generated by albacore.
  --bam file [file ...]
                        Data is in one or more sorted bam file(s).
  --cram file [file ...]
                        Data is in one or more sorted cram file(s).
  --pickle pickle       Data is a pickle file stored earlier.

EXAMPLES:
    Nanoplot --summary sequencing_summary.txt --loglength -o summary-plots-log-transformed
    NanoPlot -t 2 --fastq reads1.fastq.gz reads2.fastq.gz --maxlength 40000 --plots hex dot
    NanoPlot --color yellow --bam alignment1.bam alignment2.bam alignment3.bam --downsample 10000