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

TRhist

Finds significant tandem repeats using short reads. TRhist is a tandem repeat profiler that enable to sense and locate short tandem repeats (STRs) from billions of short reads. Information provided by the software allow user to align the flanking regions and other end read to the reference to locate the STR in the genome.

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

0 user reviews

0 user reviews

No review has been posted.

TRhist 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.

TRhist classification

TRhist specifications

Software type:
Application/Script, Package/Module
Restrictions to use:
None
Output data:
The repeat unit, length of the short tandem repeat (STR), number of mutations in the STR, flanking regions surrounding the STR and other paired-end read.
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Source code URL:
http://trhist.gi.k.u-tokyo.ac.jp/ver1.0.1/TRhist_src.zip
Interface:
Command line interface
Input format:
FASTQ
Output format:
CSV, FASTA
Programming languages:
Java
Version:
1.0.1
Requirements:
JRE
Maintained:
Yes

TRhist 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.

TRhist support

Maintainer

  • Shinichi Morishita <>

Additional information

http://trhist.gi.k.u-tokyo.ac.jp/ver1.0.1/TRhistManual.txt

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)

Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Information and Communication Engineering, Faculty of Engineering and Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

Funding source(s)

Supported by Grant-in-Aid for Scientific Research on Innovative Areas (22129008, 221S0002) (in part) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and by the Global COE program (Deciphering Biosphere from Genome Big Bang) from the MEXT.

Link to literature

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