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:
process_bam(bamfile, threads)process_fastq_plain(fastqfile, 'threads')process_fastq_rich(fastqfile)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 decosterwouter@gmail.com
FAQs
Functions to extract information from Oxford Nanopore sequencing data and alignments.
We found that nanoget demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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