Functions to extract information from Oxford Nanopore sequencing data and alignments.
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
- A standard fastq file
- A fastq file with metadata from MinKNOW or Albacore
- A sequencing_summary file generated by Albacore
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
conda install -c bioconda nanoget
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