Skip to main content

Python Modules for Next-Generation Sequencing Data Analysis.

Project description

ngslib current release: ngslib 1.1.19

Wiki page moved to GitHub.


  • numpy scientific computation

  • pysam (>0.8.2) SAM/BAM file manipulation

  • argparse (required if Python2.6 is used)

Tested on

  • Python 2.6.* (64-bit)

  • Python 2.7.* (64-bit)

  • CentOS 6.4

  • Fedora 17

  • RedHat 5.5

  • Ubuntu 12.04 (python-dev and libpng-dev are required)


From PyPI:

>>> pip install ngslib


>>> easy_install ngslib

From source:

>>> easy_install --editable  --build-directory . ngslib
>>> cd ngslib
>>> python install

Major modules

  • IO: Read various biological data

  • DB: Build DB for genomic data for fast query.

  • Pipeline: Pipelines built using wrappers of commonly used tools.

  • Bed: Genomic coordinates data format.

  • BedList: A list of Bed instances.

  • TwoBitFile: python module for retrieve fasta sequence from 2bit file.

  • BigWigFile: python module for retrieve Wiggle region from BigWig file.

  • mFile: uniform interface for input types including regular file, sys.stdin/stdout and StringFile.


>>> import ngslib
>>> for tbed in ngslib.IO.BioReader('test.bed','bed'):
        print tbed
>>> bwf = ngslib.DB('','bigwig')
>>> for wig in bwf.fetch('chr1',1000,2000):
        print wig
>>> depth = bwf.pileup('chr1',3000,4000)
>>> bwf.close()


This program is released under GPLv3 license, see LICENSE for more detail.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

ngslib-1.1.20.tar.gz (1.1 MB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page