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.

Filename, size & hash SHA256 hash help File type Python version Upload date
ngslib-1.1.20.tar.gz (1.1 MB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page