ToulligQC v2.7.1

• Added Conda environment.yml.
• Fixed bugs:
  • Corrected N50 and L50 computation (issue #28).
  • Recognized the standard barcode arrangement (BC|RB|NB|BP) in the samplesheet (issue #27).
  • Fixed barcoding for the Fastq_extractor (issue #30).
  • Fixed time format for BAM and FASTQ extractors.

ToulligQC v2.7

* Moved to Ubuntu 24.04.
* Added support for ONT samplesheet.
* ToulligQC now recognizes the barcode column name as 'barcode'.
* ToulligQC now supports irregular barcode naming; issue #22  
* Fixed bugs:
    - Pandas inplace issue for FASTQ and onedsquare summary files.
    - PlotlyJS inclusion for independent image exports.
    - Corrected read/base count histogram.
    - Handled empty lines in FASTQ file.
    - Resolved compression issue in pod5 file.
    - BAM extractor can now deal with any BAM, even if it has not been generated by Dorado.
    - Handled barcode name when it's associated with kit_barcode.

ToulligQC v2.5.2

• Adapts ToulligQC v2.5 to pandas v2.0
• Adapts ToulligQC v2.5 to numpy >v1.24
• FIX: 'barcode_arrangement' column error (v2.5.1 bug).

ToulligQC v2.6

• Support for the POD5 format.
• Handling of barcoding in BAM and FASTQ files.
• Support for Fast5 .tar files without compression.
• Fixed an issue with BAM tags extraction.
• Fixed the issue with the 'passes_filtering'-only sequencing summary.
• Fixed the bug related to numpy.bool with numpy version 1.24 or later.
• Improved compatibility with pandas 2.0.

ToulligQC 2.5

• Fixed error when no failed reads were found (Issue #20).
• Fixed error when unclassified barcodes were missing.
• FASTQ and BAM files can now be used instead of the sequencing summary file.
• Added the ability to specify a barcode range (e.g., --barcodes barcode01:barcode48).

ToulligQC 2.4

This version adds some functionality and fix a minor bugs:

• In over time graphs (read length, PHRED score and translocation speed), now fill the gaps for the 75% and 25% to avoid filling glitch.
• fix 2D density plot title style.
• Fix error when a summary file with barcode information was provided in addition of barcoding files (Issue #17), now the barcode files will be skipped with a warning message in case summary file with barcode information is provided.
• Add the selected speed and sample frequency of the run in the "Run statistics" table of the ToulligQC report.

See the changelog for more informations.

ToulligQC 2.3

This version supports Numpy 1.24 (thanks to Sean Black).
The Scatter plot of read length vs PHRED score has been replaced by a 2D density plot.
We Added bases per barcode distribution graphs.

ToulligQC 2.2.3

Bugfix version:

• Fix error when no Fast5 file is found in a directory provided as argument. Now throw an understandable error message.

ToulligQC 2.2.2

Bugfix version:

• Fix when multiple sequencing summary barcode files were available, the type of the 'barcode_arrangement' column in the dataframe was not correct.

ToulligQC 2.2.1

Bugfix version:

• Generated images were not included in the main HTML report file.