This module 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:

• 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

or

conda install -c bioconda nanoget

Copyright: 2016-2020 Wouter De Coster [email protected]