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
or
conda install -c bioconda nanoget
Copyright: 2016-2020 Wouter De Coster decosterwouter@gmail.com
1 maintainer
Metadata
1 maintainer
Release files for nanoget 1.19.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| nanoget-1.19.6.tar.gz | 26.6 kB | With provenance | Details for nanoget-1.19.6.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| nanoget-1.19.6-py3-none-any.whl | Python 3 | none | any | Details for nanoget-1.19.6-py3-none-any.whl |
Total release size: 66.5 kB
Release files / nanoget-1.19.6.tar.gz
| Download URL | nanoget-1.19.6.tar.gz |
|---|---|
| Size | 26.6 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
f900c187967af06c491cb92edc017e18b914d1c02e6d0333de2fb9a78738b6fb
|
|
BLAKE2b-256 checksum How to use checksums |
2810e71d0508565178307b44076be6bb711fa441ba425e33101f588a479ae3a5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 1, 2026.
Transparency logRelease files / nanoget-1.19.6-py3-none-any.whl
| Download URL | nanoget-1.19.6-py3-none-any.whl |
|---|---|
| Size | 39.9 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
1ef2ca3b1ab75b092918bebfa659495e7a1b550c4e336ebcc3e4e5a3db73da71
|
|
BLAKE2b-256 checksum How to use checksums |
b68aa39a8bcde36635f2d529d471a28ec4d01d77f499de607b4dd38876e2dbd5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 1, 2026.
Transparency logSecurity for nanoget 1.19.6
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
Full provenance
All 2 files in this release have been uploaded with provenance metadata.
Attestation for nanoget-1.19.6.tar.gz
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Sep 1, 2026.
Transparency logA note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
