NAME

       pycoQC  -  computes metrics and generates interactive QC plots from the sequencing summary
       report generated by Oxford Nanopore technologies basecallers

DESCRIPTION

       usage: pycoQC [-h] [--version] [--summary_file [SUMMARY_FILE ...]]

              [--barcode_file [BARCODE_FILE ...]] [--bam_file  [BAM_FILE  ...]]   [--html_outfile
              HTML_OUTFILE]   [--json_outfile   JSON_OUTFILE]   [--min_pass_qual   MIN_PASS_QUAL]
              [--min_pass_len    MIN_PASS_LEN]    [--filter_calibration]    [--filter_duplicated]
              [--min_barcode_percent     MIN_BARCODE_PERCENT]    [--report_title    REPORT_TITLE]
              [--template_file TEMPLATE_FILE] [--config_file CONFIG_FILE]  [--skip_coverage_plot]
              [--sample SAMPLE] [--default_config] [-v | -q]

       pycoQC  computes  metrics  and  generates interactive QC plots from the sequencing summary
       report generated by Oxford Nanopore technologies basecallers

       * Minimal usage

              pycoQC -f sequencing_summary.txt -o pycoQC_output.html

       * Including Guppy barcoding file + html output + json output

              pycoQC -f sequencing_summary.txt -b barcoding_sequencing.txt -o  pycoQC_output.html
              -j pycoQC_output.json

       * Including Bam file + html output

              pycoQC -f sequencing_summary.txt -a alignment.bam -o pycoQC_output.html

   optional arguments:
       -h, --help
              show this help message and exit

       --version
              show program's version number and exit

       -v, --verbose
              Increase verbosity

       -q, --quiet
              Reduce verbosity

   Input/output options:
       --summary_file [SUMMARY_FILE ...], -f [SUMMARY_FILE ...]
              Path     to    a    sequencing_summary    generated    by    Albacore    1.0.0    +
              (read_fast5_basecaller.py) / Guppy 2.1.3+ (guppy_basecaller).  One  can  also  pass
              multiple  space  separated file paths or a UNIX style regex matching multiple files
              (Required)

       --barcode_file [BARCODE_FILE ...], -b [BARCODE_FILE ...]
              Path to the barcode_file generated by Guppy 2.1.3+ (guppy_barcoder)  or  Deepbinner
              0.2.0+.  This  is  not  a required file. One can also pass multiple space separated
              file paths or a UNIX style regex matching multiple files (optional)

       --bam_file [BAM_FILE ...], -a [BAM_FILE ...]
              Path to a Bam file corresponding to reads in the summary_file.  Preferably  aligned
              with Minimap2 One can also pass multiple space separated file paths or a UNIX style
              regex matching multiple files (optional)

       --html_outfile HTML_OUTFILE, -o HTML_OUTFILE
              Path to an output html file report (required if json_outfile not given)

       --json_outfile JSON_OUTFILE, -j JSON_OUTFILE
              Path to an output json file report (required if html_outfile not given)

   Filtering options:
       --min_pass_qual MIN_PASS_QUAL
              Minimum quality to consider a read as 'pass' (default: 7)

       --min_pass_len MIN_PASS_LEN
              Minimum read length to consider a read as 'pass' (default: 0)

       --filter_calibration
              If given, reads flagged  as  calibration  strand  by  the  basecaller  are  removed
              (default: False)

       --filter_duplicated
              If  given,  duplicated  read_ids are removed but the first occurence is kept (Guppy
              sometimes outputs the same read multiple times) (default: False)

       --min_barcode_percent MIN_BARCODE_PERCENT
              Minimal percent of total reads to retain barcode label. If below, the barcode value
              is set as `unclassified` (default: 0.1)

   HTML report options:
       --report_title REPORT_TITLE
              Title to use in the html report (default: PycoQC report)

       --template_file TEMPLATE_FILE
              Jinja2 html template for the html report (default: )

       --config_file CONFIG_FILE
              Path  to a JSON configuration file for the html report.  If not provided, looks for
              it in ~/.pycoQC and ~/.config/pycoQC/config. If it's still not found, falls back to
              default parameters. The first level keys are the names of the plots to be included.
              The second level keys  are  the  parameters  to  pass  to  each  plotting  function
              (default: )")

       --skip_coverage_plot
              Skip  the  coverage  plot  in  HTML  report.  Useful  when  using  a reference file
              containing many sequences, i.e.  transcriptome (default: False)

   Other options:
       --sample SAMPLE
              If not None a n number of reads will be randomly selected  instead  of  the  entire
              dataset for ploting function (deterministic sampling) (default: 100000)

       --default_config, -d
              Print  default  configuration  file.  Can  be used to generate a template JSON file
              (default: False)

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.