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.

pycoQC 2.5.2                                      December 2020                                        PYCOQC(1)