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

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