nanoget

September 19, 2023 · View on GitHub

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

FUNCTIONS

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.

INSTALLATION

pip install nanoget

conda install -c bioconda nanoget