pyc
pycoQC
pypi i pycoQC
pyc

pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

by Adrien Leger

2.5.2 (see all)License:GPLv3
pypi i pycoQC
Readme

pycoQC v2.5.2

pycoQC

JOSS DOI Gitter chat GitHub license Language

PyPI version Downloads

Anaconda Version Anaconda Downloads

install with bioconda Bioconda Downloads

Build Status Codacy Badge


PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data

PycoQC relies on the sequencing_summary.txt file generated by Albacore and Guppy, but if needed it can also generate a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices, basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. Python 2 is not supported. For a quick introduction see tutorial by Tim Kahlke available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html

Full documentation is available at https://adrienleger.com/pycoQC

summary

reads_len_1D_example]

reads_len_1D_example]

reads_qual_len_2D_example

channels_activity

output_over_time

qual_over_time

len_over_time

align_len

align_score

align_score_len_2D

alignment_coverage

alignment_rate

alignment_summary

Example HTML reports

Example JSON reports

Disclaimer

Please be aware that pycoQC is a research package that is still under development.

It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.

Thank you

Classifiers

  • Development Status :: 3 - Alpha
  • Intended Audience :: Science/Research
  • Topic :: Scientific/Engineering :: Bio-Informatics
  • License :: OSI Approved :: GNU General Public License v3 (GPLv3)
  • Programming Language :: Python :: 3

licence

GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html)

Copyright © 2020 Adrien Leger & Tommaso Leonardi

Authors

GitHub Stars

151

LAST COMMIT

7mos ago

MAINTAINERS

1

CONTRIBUTORS

7

OPEN ISSUES

7

OPEN PRs

0
VersionTagPublished
2.5.2
2yrs ago
2.5.1
2yrs ago
2.5.0.23
2yrs ago
2.5.0.21
2yrs ago
No alternatives found
No tutorials found
Add a tutorial