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 nanogetor
conda install -c bioconda nanoget