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Functions to extract information from Oxford Nanopore sequencing data and alignments.

Project description


This module provides functions to extract useful metrics from Oxford Nanopore sequencing reads and alignments.

Twitter URL install with conda Build Status


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

  • A sorted bam file process_bam(bamfile, threads)
  • A standard fastq file process_fastq_plain(fastqfile, 'threads')
  • A fastq file with metadata from MinKNOW or Albacore process_fastq_rich(fastqfile)
  • A 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.


pip install nanoget

install with conda

conda install -c bioconda nanoget

Copyright: 2016-2020 Wouter De Coster

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