---
name: "pycoQC"
section: "1"
platform: "linux"
package: "pycoqc"
version: "2.5.2+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pycoQC"
---

# pycoQC(1)

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

## 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.