Functions to extract information from Oxford Nanopore sequencing data and alignments.

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nanoget

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

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This version

1.19.4

Dec 4, 2025

1.19.3

Sep 19, 2023

1.19.1

Jul 1, 2023

1.19.0

Jul 1, 2023

1.18.1

Sep 28, 2022

1.18.0

Sep 2, 2022

1.17.0

Aug 30, 2022

1.16.1

Mar 20, 2021

1.16.0

Mar 19, 2021

1.15.0

Aug 19, 2020

1.14.0

Jul 22, 2020

1.13.2

Jun 17, 2020

1.13.1

May 30, 2020

1.13.0

May 16, 2020

1.12.2

May 4, 2020

1.12.1

Mar 2, 2020

1.12.0

Dec 3, 2019

1.11.0

Nov 21, 2019

1.10.0

Nov 20, 2019

1.9.1

Oct 22, 2019

1.9.0

Aug 27, 2019

1.8.0

Mar 15, 2019

1.7.7

Jan 29, 2019

1.7.6

Nov 23, 2018

1.7.5

Nov 19, 2018

1.7.4

Sep 15, 2018

1.7.3

Sep 12, 2018

1.7.2

Aug 9, 2018

1.7.1

Aug 9, 2018

1.7.0

Aug 9, 2018

1.6.0

Jul 20, 2018

1.5.2

Jun 27, 2018

1.5.0

Feb 18, 2018

1.4.0

Feb 7, 2018

1.3.0

Jan 17, 2018

1.2.2

Jan 10, 2018

1.2.1

Dec 22, 2017

1.2.0

Dec 5, 2017

1.1.0

Nov 15, 2017

1.0.2

Nov 7, 2017

1.0.0

Nov 3, 2017

0.19.3

Nov 2, 2017

0.19.0

Oct 27, 2017

0.18.0

Oct 26, 2017

0.17.0

Oct 26, 2017

0.16.1

Oct 26, 2017

0.15.0

Oct 20, 2017

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Oct 10, 2017

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Oct 9, 2017

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Sep 22, 2017

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Sep 21, 2017

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Sep 21, 2017

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Aug 23, 2017

0.11.7

Aug 18, 2017

0.11.5

Jul 28, 2017

0.11.4

Jul 27, 2017

0.11.3

Jul 27, 2017

0.11.2

Jul 27, 2017

0.11.0

Jul 25, 2017

0.10.6

Jul 15, 2017

0.10.1

Jun 16, 2017

0.10.0

Jun 16, 2017

0.9.8

Jun 14, 2017

0.9.7

Jun 14, 2017

0.9.6

Jun 9, 2017

0.9.5

Jun 5, 2017

0.9.4

Jun 5, 2017

0.9.3

Jun 5, 2017

0.9.2

Jun 5, 2017

0.9.1

Jun 5, 2017

0.9.0

Jun 5, 2017

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