nanoget 0.11.4

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:

- A sorted bam file processBam(bamfile, threads)

- A standard fastq file processFastqPlain(fastqfile)

- A fastq file with metadata from MinKNOW or Albacore processFastq_rich(fastqfile)

- A sequencing_summary file generated by Albacore processSummary(sequencing_summary.txt)

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.