Package: python3-nanoget-examples (1.19.3-1)

[ Source: python-nanoget  ]

example data for python3-nanoget (dealing with Oxford Nanopore data)

The Python3 module nanoget provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments.

Data can be presented in the following formats, using the following functions:

 * sorted bam file process_bam(bamfile, threads)
 * standard fastq file process_fastq_plain(fastqfile, 'threads')
 * fastq file with metadata from MinKNOW or Albacore
   process_fastq_rich(fastqfile)
 * sequencing_summary file generated by Albacore
   process_summary(sequencing_summary.txt, 'readtype')

Fastq files can be compressed using gzip, bzip2 or bgzip. The data is returned as a pandas DataFrame with standardized headernames for convenient extraction. The functions perform logging while being called and extracting data.

This package just contains an example script and the data to run the example.

Other Packages Related to python3-nanoget-examples

• enh: python3-nanoget

  extract information from Oxford Nanopore sequencing data and alignments

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