[ Bron: python-nanoget ]
Pakket: python3-nanoget (1.12.2-4)
Verwijzigingen voor python3-nanoget
Debian bronnen:
Het bronpakket python-nanoget downloaden:
- [python-nanoget_1.12.2-4.dsc]
- [python-nanoget_1.12.2.orig.tar.gz]
- [python-nanoget_1.12.2-4.debian.tar.xz]
Beheerders:
Externe bronnen:
- Homepage [github.com]
Vergelijkbare pakketten:
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.
Andere aan python3-nanoget gerelateerde pakketten
|
|
|
|
-
- dep: python3
- interactive high-level object-oriented language (default python3 version)
-
- dep: python3-biopython
- Python3 library for bioinformatics
-
- dep: python3-nanomath
- simple math function for other Oxford Nanopore processing scripts
-
- dep: python3-numpy
- Fast array facility to the Python 3 language
-
- dep: python3-pandas
- data structures for "relational" or "labeled" data
-
- dep: python3-pysam
- interface for the SAM/BAM sequence alignment and mapping format (Python 3)