5.3. read length histograms pacbio dataΒΆ

QC pacbio example

First, let us get a data set example. Note the .bam extension

from sequana import sequana_data
dataset  = sequana_data("test_pacbio_subreads.bam")

Create a sequana.pacbio.BAMPacbio instance

from sequana.pacbio import BAMPacbio
qc = BAMPacbio(dataset)

plot the histogram of read length

qc.hist_len()
../_images/sphx_glr_plot_qc_pacbio_001.png

plot the histogram of the SNRs for each base

qc.hist_snr()
../_images/sphx_glr_plot_qc_pacbio_002.png

Total running time of the script: (0 minutes 0.618 seconds)

Download Python source code: plot_qc_pacbio.py
Download IPython notebook: plot_qc_pacbio.ipynb