PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data
Project description
![pycoQC](docs/pictures/pycoQC_long.svg)
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Full documentation is available at https://a-slide.github.io/pycoQC/
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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.
# Gallery
Click on a picture to access an online interactive version editable with [plotly chart studio](https://plot.ly/online-chart-maker/)
[![summary](./docs/pictures/summary.gif)](https://plot.ly/~aleg/16/)
[![reads_len_1D_example](./docs/pictures/reads_len_1D.gif)](https://plot.ly/~aleg/2/distribution-of-read-length/)
[![reads_len_1D_example](./docs/pictures/reads_qual_1D.gif)](https://plot.ly/~aleg/66/distribution-of-read-quality-scores/)
[![reads_qual_len_2D_example](./docs/pictures/reads_qual_len_2D.gif)](https://plot.ly/~aleg/3/mean-read-quality-per-sequence-length/)
[![channels_activity](./docs/pictures/channels_activity.gif)](https://plot.ly/~aleg/4/output-per-channel-over-experiment-time/)
[![output_over_time](./docs/pictures/output_over_time.gif)](https://plot.ly/~aleg/5/output-over-experiment-time/)
[![qual_over_time](./docs/pictures/qual_over_time.gif)](https://plot.ly/~aleg/6/mean-read-quality-over-experiment-time/)
[![len_over_time](./docs/pictures/len_over_time.gif)](https://plot.ly/~aleg/28/read-length-over-experiment-time/)
[![barcode_counts](./docs/pictures/barcode_counts.gif)](https://plot.ly/~aleg/7/percentage-of-reads-per-barcode/)
## Example HTML reports
[Albacore-1.2.1_basecall-1D-DNA](https://a-slide.github.io/pycoQC/demo/data/output/Albacore-1.2.1_basecall-1D-DNA.html)
[Albacore-1.7.0_basecall-1D-DNA](https://a-slide.github.io/pycoQC/demo/data/output/Albacore-1.7.0_basecall-1D-DNA.html)
[Albacore-2.1.10_basecall-1D-DNA](https://a-slide.github.io/pycoQC/demo/data/output/Albacore-2.1.10_basecall-1D-DNA.html)
[Albacore_all_RNA](https://a-slide.github.io/pycoQC/demo/data/output/Albacore_all_RNA.html)
[Guppy-2.1.3_basecall-1D_DNA_barcode](https://a-slide.github.io/pycoQC/demo/data/output/Guppy-2.1.3_basecall-1D_DNA_barcode.html)
[Guppy-2.1.3_basecall-1D_RNA](https://a-slide.github.io/pycoQC/demo/data/output/Guppy-2.1.3_basecall-1D_RNA.html)
## Authors
Adrien Leger - aleg {at} ebi.ac.uk
Tommaso Leonardi - tom {at} tleo.io
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