pycoQC, interactive quality control for Oxford Nanopore Sequencing - https://github.com/a-slide/pycoQC/releases/tag/2.5.2

Scientific Software - Peer-reviewed - Python
Published by a-slide about 5 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.5.0.23

• Adding multi Fast5 support to Fast5toseqsummary #49 thanks to @snajder-r contribution Made Fast5toseqsummary work on multi-fast5 files #115
• Add link to @timkahlke tutorial in documentation
• Add bioconda badge

Scientific Software - Peer-reviewed - Python
Published by a-slide over 5 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.5.0.21

Scientific Software - Peer-reviewed - Python
Published by a-slide almost 6 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - 2.5.0.3

This major update add new functionalities to pycoQC and improve a number of existing ones:

• BAM files parsing
• 8 new alignment specific plots
• Updated json format including alignment information when available
• Option to filter out duplicated reads due to Guppy over-calling (--filter_duplicated)
• New tool to split summary sequencing file by barcodes
• Improve HTML report layout and add list of source files at the end
• Update documentation and demo notebooks
• Add Codacity integration

Scientific Software - Peer-reviewed - Python
Published by a-slide over 6 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.3.1.6 Stable

This release is mainly a fix for promethion flowcells for which pycoQC used to generate massive report files. It's much better no, but is the size is still an issue it is recommended to drop out the channel activity plot

Scientific Software - Peer-reviewed - Python
Published by a-slide over 6 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.2.4 stable

• Rewrite argparse including better handling of input file regex

• Rewrite doc with mkdocs.

• Add methods to generate data dict and json file on top of HTML

• Summary can now optionally split per run_id or barcode

Scientific Software - Peer-reviewed - Python
Published by a-slide almost 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.2.3 stable

Minor patch for windows compatibility

Scientific Software - Peer-reviewed - Python
Published by a-slide almost 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.2.2 stable

This release include minor text edits for the JOSS paper. We also added a gitter chatroom

Scientific Software - Peer-reviewed - Python
Published by a-slide almost 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.2.1 stable

Minor fixes and improved documentation as part as JOSS submission

Scientific Software - Peer-reviewed - Python
Published by a-slide about 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v2.2.0 stable

• Fix minor bugs
• Improve documentation
• Update test datasets
• Include draft of paper to be submitted to JOSS

Scientific Software - Peer-reviewed - Python
Published by a-slide about 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - 2.1alpha2

Implement manual Summary sequencing file generation

Scientific Software - Peer-reviewed - Python
Published by a-slide about 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - pycoQC 2.0 alpha6

This release contains a first prototype of command line interface generating a beautiful HTML report (for people who don't like Jupyter).

In addition we fixed the default behaviour of pycoQC to generate empty plots that then needed to be activated by clicking on one of the button.

Scientific Software - Peer-reviewed - Python
Published by a-slide over 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - pycoQC 2.0 alpha5

This new version is a major disruptive package update not retro compatible with previous released versions. The last stable v1 version is archived in a separate stalled branch that will not be maintained any more (https://github.com/a-slide/pycoQC/tree/v1).

This major update includes the following: * Slight performance improvement * Transition from matplolib/seaborn to plotly to generate beautiful interactive plots * Changes in plots in response to the issues raised in pycoQC 1 (issues closed now) * pipy packaging * Usage is now available in an interactive online jupyter notebook + static HTML version * Multiple Sequencing summary files can now be provided * Add barcode support * Use logging module + custom exception

Basically it is a 90% rewriting of the entire package

Scientific Software - Peer-reviewed - Python
Published by a-slide over 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - Relase final version of legacy version v1

No changes, except updating of installation instructions for v1 legacy version

Scientific Software - Peer-reviewed - Python
Published by a-slide over 7 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.1.alpha2

Add barcode plotting functionality

Scientific Software - Peer-reviewed - Python
Published by a-slide almost 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.1.alpha2

Just add DOI for automatic archiving and citations

Scientific Software - Peer-reviewed - Python
Published by a-slide about 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.1.alpha1

Re-factoring, update to extract more info from Albacore 2.0+ and add extra options for plots

Scientific Software - Peer-reviewed - Python
Published by a-slide about 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.0.alpha

First alpha release, including documentation and tests

Scientific Software - Peer-reviewed - Python
Published by a-slide over 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.0.dev3

Minor improvements and additional capabilities

Scientific Software - Peer-reviewed - Python
Published by a-slide over 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.0.dev2

Add new function * readslenquality

Update tests and readme

Scientific Software - Peer-reviewed - Python
Published by a-slide over 8 years ago

pycoQC, interactive quality control for Oxford Nanopore Sequencing - v1.0.dev1

Initial release of pycoQC containing 5 plotting functions * channelsactivity * meanqualdistribution * outputovertime * qualityovertime * readslen_distribution

Scientific Software - Peer-reviewed - Python
Published by a-slide over 8 years ago