Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

Homozygous Stretch Identifier from next-generation sequencing data HomSI

Identifies homozygous stretches using new generation sequencing (NGS) data. HomSI was designed to define homozygous stretches in consanguineous families from NGS data. To identify and visualize the homozygous stretches, the software processes each variant and generates several graphs. It was evaluated using both a simulated dataset generated and a real dataset of three disease genes within the homozygous regions, which have been previously identified using a combination of exome and single-nucleotide polymorphism (SNP) microarray data.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community
Sort by:

1 user review

1 user review

moyaro2000's avatar image

moyaro2000

The homozygosity Stretch Identifier (HomSI) has the stringent settings of 5Mb window size and 10 kb sliding size that permits the capturing of wide spectrum of signatures of selections. Additionally, the resolution of identified signatures of selection by HomSI can be very high to the magnitude of 1 Kilo base pairs. This high resolution facilitates a better analysis of the selective sweep characteristics in relation to the specific genomic coordinates across every part of the genome.

HomSI forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

HomSI classification

HomSI specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux
License:
Academic Free License version 3.0
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input format:
VCF
Programming languages:
Java
Computer skills:
Advanced
Requirements:
JRE

HomSI distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

HomSI support

Maintainer

  • Burcu Bakir-Gungor <>

Additional information

Tutorial: http://www.igbam.bilgem.tubitak.gov.tr/en/softwares/HomSI/tutorial.html

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Advanced Genomics and Bioinformatics Research Center, The Scientific and Technological Research Council of Turkey (TUBITAK-BILGEM),Gebze, Kocaeli, Turkey; Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, Turkey

Funding source(s)

Supported by the Turkish State Planning Organization Research Grants, Grant Number: 108S420, UEKAE, BILGEM and The Scientific and Technology Research Council of Turkey (TUBITAK), Grant Number: K030-T439.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.