.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH PYCOQC "1" "December 2020" "pycoQC 2.5.2" "User Commands"
.SH NAME
pycoQC \- computes metrics and generates interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecallers
.SH DESCRIPTION
usage: pycoQC [\-h] [\-\-version] [\-\-summary_file [SUMMARY_FILE ...]]
.IP
[\-\-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 | \fB\-q]\fR
.PP
pycoQC computes metrics and generates interactive QC plots from the sequencing summary
report generated by Oxford Nanopore technologies basecallers
.PP
* Minimal usage
.IP
pycoQC \fB\-f\fR sequencing_summary.txt \fB\-o\fR pycoQC_output.html
.PP
* Including Guppy barcoding file + html output + json output
.IP
pycoQC \fB\-f\fR sequencing_summary.txt \fB\-b\fR barcoding_sequencing.txt \fB\-o\fR pycoQC_output.html \fB\-j\fR pycoQC_output.json
.PP
* Including Bam file + html output
.IP
pycoQC \fB\-f\fR sequencing_summary.txt \fB\-a\fR alignment.bam \fB\-o\fR pycoQC_output.html
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Increase verbosity
.TP
\fB\-q\fR, \fB\-\-quiet\fR
Reduce verbosity
.SS "Input/output options:"
.TP
\fB\-\-summary_file\fR [SUMMARY_FILE ...], \fB\-f\fR [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)
.TP
\fB\-\-barcode_file\fR [BARCODE_FILE ...], \fB\-b\fR [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)
.TP
\fB\-\-bam_file\fR [BAM_FILE ...], \fB\-a\fR [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)
.TP
\fB\-\-html_outfile\fR HTML_OUTFILE, \fB\-o\fR HTML_OUTFILE
Path to an output html file report (required if
json_outfile not given)
.TP
\fB\-\-json_outfile\fR JSON_OUTFILE, \fB\-j\fR JSON_OUTFILE
Path to an output json file report (required if
html_outfile not given)
.SS "Filtering options:"
.TP
\fB\-\-min_pass_qual\fR MIN_PASS_QUAL
Minimum quality to consider a read as 'pass' (default:
7)
.TP
\fB\-\-min_pass_len\fR MIN_PASS_LEN
Minimum read length to consider a read as 'pass'
(default: 0)
.TP
\fB\-\-filter_calibration\fR
If given, reads flagged as calibration strand by the
basecaller are removed (default: False)
.TP
\fB\-\-filter_duplicated\fR
If given, duplicated read_ids are removed but the
first occurence is kept (Guppy sometimes outputs the
same read multiple times) (default: False)
.TP
\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT
Minimal percent of total reads to retain barcode
label. If below, the barcode value is set as
`unclassified` (default: 0.1)
.SS "HTML report options:"
.TP
\fB\-\-report_title\fR REPORT_TITLE
Title to use in the html report (default: PycoQC
report)
.TP
\fB\-\-template_file\fR TEMPLATE_FILE
Jinja2 html template for the html report (default: )
.TP
\fB\-\-config_file\fR 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: )")
.TP
\fB\-\-skip_coverage_plot\fR
Skip the coverage plot in HTML report. Useful when
using a reference file containing many sequences, i.e.
transcriptome (default: False)
.SS "Other options:"
.TP
\fB\-\-sample\fR 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)
.TP
\fB\-\-default_config\fR, \fB\-d\fR
Print default configuration file. Can be used to
generate a template JSON file (default: False)
.SH AUTHOR
 This manpage was written by Nilesh Patra for the Debian distribution and
 can be used for any other usage of the program.