Package: python3-nanoget (1.19.3-1)

[ Source: python-nanoget  ]

extract information from Oxford Nanopore sequencing data and alignments

The Python3 module nanoget 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:

 * sorted bam file process_bam(bamfile, threads)
 * standard fastq file process_fastq_plain(fastqfile, 'threads')
 * fastq file with metadata from MinKNOW or Albacore
   process_fastq_rich(fastqfile)
 * 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.

Other Packages Related to python3-nanoget

• dep: python3

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• dep: python3-biopython

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• dep: python3-nanomath

  simple math function for other Oxford Nanopore processing scripts

• dep: python3-numpy

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• dep: python3-pandas (>= 2.0.0)

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• dep: python3-pysam

  interface for the SAM/BAM sequence alignment and mapping format (Python 3)

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