Metadata-Version: 2.1
Name: pycoQC
Version: 2.5.1
Summary: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data
Home-page: https://github.com/a-slide/pycoQC
Author: Adrien Leger & Tommaso Leonardi
Author-email: aleg@ebi.ac.uk
License: GPLv3
Description: ![pycoQC](https://raw.githubusercontent.com/a-slide/pycoQC/master/docs/pictures/pycoQC_long.png)
        
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        ---
        
        **Full documentation is available at https://a-slide.github.io/pycoQC/**
        
        ---
        
        **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 generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. **Python 2 is not supported**.
        
        Great tutorial with detailed explanations by [Tim Kahlke](https://github.com/timkahlke) available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html
        
        ## Gallery
        
        ![summary](./docs/pictures/summary.gif)
        
        ![reads_len_1D_example](./docs/pictures/reads_len_1D.gif)]
        
        ![reads_len_1D_example](./docs/pictures/reads_qual_1D.gif)]
        
        ![reads_qual_len_2D_example](./docs/pictures/reads_qual_len_2D.gif)
        
        ![channels_activity](./docs/pictures/channels_activity.gif)
        
        ![output_over_time](./docs/pictures/output_over_time.gif)
        
        ![qual_over_time](./docs/pictures/qual_over_time.gif)
        
        ![len_over_time](./docs/pictures/len_over_time.gif)
        
        ![align_len](./docs/pictures/align_len_1D.gif)
        
        ![align_score](./docs/pictures/align_score_1D.gif)
        
        ![align_score_len_2D](./docs/pictures/align_score_len_2D.gif)
        
        ![alignment_coverage](./docs/pictures/alignment_coverage.gif)
        
        ![alignment_rate](./docs/pictures/alignment_rate.gif)
        
        ![alignment_summary](./docs/pictures/alignment_summary.gif)
        
        ## Example HTML reports
        
        * [Albacore_all_RNA](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore_all_RNA.html)
        
        * [Guppy-2.1.3_basecall-1D_RNA](https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.html)
        
        * [Guppy-2.3_basecall-1D_alignment-DNA](https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.html)
        
        * [Albacore-1.2.1_basecall-1D-DNA](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.2.1_basecall-1D-DNA.html)
        
        * [Guppy-2.1.3_basecall-1D_DNA_barcode](https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_DNA_barcode.html)
        
        * [Albacore-1.7.0_basecall-1D-DNA_API](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.html)
        
        * [Albacore-2.1.10_basecall-1D-DNA](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-2.1.10_basecall-1D-DNA.html)
        
        * [Albacore-1.7.0_basecall-1D-DNA](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA.html)
        
        ## Example JSON reports
        
        * [Guppy-2.3_basecall-1D_alignment-DNA](https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.json)
        
        * [Guppy-2.1.3_basecall-1D_RNA](https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.json)
        
        * [Albacore-1.7.0_basecall-1D-DNA_API](https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.json)
        
        ## Authors
        
        * Adrien Leger - aleg {at} ebi.ac.uk
        
        * Tommaso Leonardi - tom {at} tleo.io
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.5
Description-Content-Type: text/markdown
