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pycoQC, interactive quality control for Oxford Nanopore Sequencing

pycoQC, interactive quality control for Oxford Nanopore Sequencing - Published in JOSS (2019)

https://github.com/a-slide/pycoqc

Science Score: 95.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org, zenodo.org
  • ✓
    Committers with academic emails
    3 of 6 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

computing-metrics generates-plots jupyter-notebook nanopore

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 283
  • Watchers: 4
  • Forks: 40
  • Open Issues: 21
  • Releases: 21
Archived
Topics
computing-metrics generates-plots jupyter-notebook nanopore
Created over 8 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

pycoQC v2.5.2

PycoQC in not maintained anymore, If you are interested in continuing the delelopment of this repository please contact me to discuss an eventual ownership transfer (adrien.leger at protonmail dot com)

pycoQC

JOSS DOI Gitter chat GitHub license Language

PyPI version Downloads

Anaconda Version Anaconda Downloads

install with bioconda Bioconda Downloads

Build Status

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/LongReadtutorials/QCP.html

Full documentation is available at https://a-slide.github.io/pycoQC

Gallery

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

  • Adrien Leger & Tommaso Leonardi

Owner

  • Name: Adrien Leger
  • Login: a-slide
  • Kind: user
  • Location: Oxford, UK
  • Company: @nanoporetech

Research scientist at Oxford Nanopore Technologies

JOSS Publication

pycoQC, interactive quality control for Oxford Nanopore Sequencing
Published
February 28, 2019
DOI
Volume 4, Issue 34, Page 1236
Authors
Adrien Leger ORCID
European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK
Tommaso Leonardi ORCID
Gurdon Institute, Cambridge, Cambridgeshire, UK, Center for Genomic Science IIT\@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy
Editor
Pjotr Prins ORCID
Tags
python3 plots metrics nanopore sequencing interactive quality control
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GitHub Events

Total
  • Watch event: 19
  • Push event: 1
  • Fork event: 1
Last Year
  • Watch event: 19
  • Push event: 1
  • Fork event: 1

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 381
  • Total Committers: 6
  • Avg Commits per committer: 63.5
  • Development Distribution Score (DDS): 0.066
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
a-slide a****g@e****k 356
Tommaso Leonardi t****m@i****z 17
Jamin c****u@g****m 3
Jon Sanders j****s@o****u 3
Daniel S. Katz d****z@i****g 1
Rene Snajder r****r@d****e 1
Committer Domains (Top 20 + Academic)
dkfz.de: 1 ieee.org: 1 oeb.harvard.edu: 1 itm6.xyz: 1 ebi.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 72
  • Total pull requests: 37
  • Average time to close issues: 2 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 44
  • Total pull request authors: 6
  • Average comments per issue: 3.04
  • Average comments per pull request: 0.19
  • Merged pull requests: 36
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 18 hours
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • a-slide (16)
  • thierryjanssens (4)
  • mbhall88 (3)
  • inijman (3)
  • sklages (3)
  • splaisan (2)
  • apeltzer (2)
  • unique379r (2)
  • wuy24 (1)
  • callumparr (1)
  • hrpelg (1)
  • chanster-j (1)
  • ktenpatel (1)
  • dlbowie0 (1)
  • skchronicles (1)
Pull Request Authors
  • a-slide (31)
  • tleonardi (2)
  • godotgildor (1)
  • snajder-r (1)
  • liujamin (1)
  • danielskatz (1)
Top Labels
Issue Labels
enhancement (17) Waiting validation (4) Low_priority (3) help wanted (1) wontfix (1) bug (1) reminder (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 3
  • Total downloads:
    • pypi 451 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 58
  • Total maintainers: 1
proxy.golang.org: github.com/a-slide/pycoQC
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/a-slide/pycoqc
  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 6 months ago
pypi.org: pycoqc

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

  • Versions: 50
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 451 Last month
Rankings
Stargazers count: 4.6%
Forks count: 6.5%
Downloads: 9.2%
Dependent packages count: 10.1%
Average: 19.5%
Dependent repos count: 67.2%
Maintainers (1)
aleg
Last synced: 6 months ago

Dependencies

.versipy/setup.py pypi
  • dependency_1__ *
  • dependency_2__ *
  • dependency_3__ *
  • dependency_4__ *
  • dependency_5__ *
  • dependency_6__ *
  • dependency_7__ *
  • dependency_8__ *
setup.py pypi
  • h5py >=3.1
  • jinja2 >=2.10
  • numpy >=1.19
  • pandas >=1.1
  • plotly ==4.1.0
  • pysam >=0.16
  • scipy >=1.5
  • tqdm >=4.54